--- /dev/null
+# Makefile for construction of databases that Jpred uses.
+# The pdb make target has been over documented so as to provide
+# explanation of the method behind the madness.
+# All variables are defined at the top of the file, and then targets
+# are defined afterwards
+
+# Suffixes created by BLAST, ptm is also created, but I think this is
+# a temporary file, so is mentioned explicitly in the clean target
+BLAST_SUFFIX = .phr .pin .psd .psi .psq
+
+# Specifically add path for some of the commands so we know we'll
+# find them
+PATH := $(PATH):/r0/www_servers/jpred/jpred_bin:/site/Linux/bin
+
+# Define commands that occur multiple times
+# The wget command means that you have to give the output location first,
+# then the target
+WGET = wget -N -t 10
+FORMATDB = formatdb -o T -i
+
+# Variables specific for PDB stuff
+# URL to get the file from
+PDB_URL = ftp://ftp.ebi.ac.uk/pub/databases/msd/pdb_aa.fasta
+PDB_FILE = $(notdir $(PDB_URL))
+# Target path to download to
+PDB_FASTA = pdb.fasta
+# Files created by running formatdb on $(PDB_FASTA)
+PDB_BLAST = $(addprefix $(PDB_FASTA), $(BLAST_SUFFIX))
+# Directory to install the files into
+#PDB_TARGET = /r0/www_servers/jpred/databases/pdb
+PDB_TARGET = /tmp/jpred/databases/pdb
+# The target paths of the files that are to be installed
+PDB_INSTALL = $(addprefix $(PDB_TARGET)/, $(PDB_BLAST) $(PDB_FASTA))
+
+# Variables specific for SWALL
+SP_URL = ftp://ftp.ebi.ac.uk/pub/databases/sp_tr_nrdb/fasta/sprot.fas.gz
+SP_FILE = $(notdir $(SP_URL))
+TREMBL_URL = ftp://ftp.ebi.ac.uk/pub/databases/sp_tr_nrdb/fasta/trembl.fas.gz
+TREMBL_FILE = $(notdir $(TREMBL_URL))
+
+SWALL_FASTA = swall.fasta
+SWALL_INDX = swall.jidx
+SWALL_FILT = swall.filt
+SWALL_BLAST = $(addprefix $(SWALL_FILT), $(BLAST_SUFFIX))
+SWALL_TARGET = /tmp/jpred/cluster/packages/jpred_swall
+SWALL_INSTALL = $(addprefix $(SWALL_TARGET)/, $(SWALL_BLAST) $(SWALL_FASTA) $(SWALL_FILT))
+
+######################################################################
+all: pdb.db swall.db
+
+######################################################################
+# PDB FASTA seqeunce database
+
+# Heirarchy of dependancies (indentation denotes dependancy):
+# /installation/dir/pdb.fasta{,.{phr,pin,psd,psi,psq}}
+# pdb_wget
+# pdb.fasta{.{phr,pin,psd,psi,psq}}
+# pdb.fasta
+# pdb_aa.fasta
+# pdb_wget creates pdb_aa.fasta
+
+# This states that the PDB target depends upon the pdb_wget target and
+# the files in the variable $(PDB_INSTALL), this is the group of formatdb
+# index files and the original FASTA file used to create them in the
+# installation directory
+pdb.db: pdb_wget $(PDB_INSTALL)
+
+# This installs the files into the final directory
+$(PDB_INSTALL): $(PDB_BLAST)
+ mkdir -p $(PDB_TARGET)
+ install -m 644 $(PDB_BLAST) $(PDB_FASTA) $(PDB_TARGET)
+
+# Do BLAST DB formating. This depends on a group of files, so if any of
+# them are deleted/too old, then they're reformated.
+$(PDB_BLAST): $(PDB_FASTA)
+ $(FORMATDB) $(PDB_FASTA)
+
+$(PDB_FASTA): $(PDB_FILE)
+ cp $(PDB_FILE) $(PDB_FASTA)
+
+# This is a phony rule that's always executed, in this case it's to check
+# whether a newer version of the PDB FASTA file has been deposited on the
+# FTP site.
+# It has to be a phony rule as if it's made a normal rule that depends
+# on the file that's downloaded, its always considered upto date and the
+# wget command isn't run.
+.PHONY: pdb_wget
+pdb_wget:
+ $(WGET) $(PDB_FASTA) $(PDB_URL)
+
+######################################################################
+
+swall.db: sp_wget trembl_wget $(SWALL_INSTALL)
+
+$(SWALL_INSTALL): $(SWALL_BLAST) $(SWALL_FASTA) $(SWALL_FILT) $(SWALL_INDX)
+ mkdir -p $(SWALL_TARGET)
+ install -m 644 $(SWALL_BLAST) $(SWALL_FASTA) $(SWALL_FILT) $(SWALL_INDX) $(SWALL_TARGET)
+
+$(SWALL_BLAST): $(SWALL_FILT)
+ $(FORMATDB) $(SWALL_FILT)
+
+# This next line defines a temporary variable for the target
+$(SWALL_FILT): TMP_FILE := $(shell tempfile -d /r0/scratch)
+$(SWALL_FILT): $(SWALL_FASTA)
+ seg $(SWALL_FASTA) 12 2.2 2.5 -x > $(TMP_FILE)
+ ~/src/helixfilt/helixfilt $(TMP_FILE) > $(SWALL_FILT)
+ rm $(TMP_FILE)
+
+$(SWALL_INDX): $(SWALL_FASTA)
+ db_dbmindex $(SWALL_FASTA) $(SWALL_INDX)
+
+$(SWALL_FASTA): $(SP_FILE) $(TREMBL_FILE)
+ gzip -c -d $(SP_FILE) > $(SWALL_FASTA)
+ gzip -c -d $(TREMBL_FILE) >> $(SWALL_FASTA)
+
+$(SP_FILE): sp_wget
+
+$(TREMBL_FILE): trembl_wget
+
+.PHONY: sp_wget
+sp_wget:
+ $(WGET) $(SP_URL)
+
+.PHONY: trembl_wget
+trembl_wget:
+ $(WGET) $(TREMBL_URL)
+
+######################################################################
+clean:
+ -rm $(SWALL_FASTA) $(SWALL_INDX) $(SWALL_FILT) $(SWALL_BLAST)
+ -rm $(PDB_FASTA) $(PDB_BLAST)
+ -rm formatdb.log *.ptm
+
+distclean: clean
+ -rm $(PDB_FILE) $(SP_FILE) $(TREMBL_FILE)
+
+installclean:
+ -rm -r $(SWALL_TARGET)
+ -rm -r $(PDB_TARGET)
--- /dev/null
+#!/usr/bin/perl
+
+=head1 NAME
+
+arco_stats.pl - script to collate SGE job stats from ARCo
+
+=cut
+
+use strict;
+use warnings;
+
+use Getopt::Long;
+use Pod::Usage;
+use File::Basename;
+use GD::Graph::bars;
+use DBI;
+
+# path for nicer fonts for the graph labels
+my $FONTPATH = "/homes/www-jpred/live/public_html/fonts/";
+my @month = qw( Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec );
+my $user = 'www-jpred';
+my $out;
+my $xDim = 700;
+my $yDim = 400;
+my $showPlot = 0;
+my $showCSV = 1;
+my $runStats = 0;
+my $quiet = 0;
+my $help;
+my $man;
+
+GetOptions(
+ 'user=s' => \$user,
+ 'x=i' => \$xDim,
+ 'y=i' => \$yDim,
+ 'plot!' => \$showPlot,
+ 'csv!' => \$showCSV,
+ 'run-stats=i' => \$runStats,
+ 'out=s' => \$out,
+ 'quiet' => \$quiet,
+ 'man' => \$man,
+ 'help|?' => \$help,
+) or pod2usage();
+
+pod2usage( -verbose => 2 ) if ($man);
+pod2usage( -verbose => 1 ) if ($help);
+
+my $dbh = DBI->connect( "dbi:Pg:host=postgres.compbio.dundee.ac.uk;dbname=arco", 'account', 'saffron' ) or die "ERROR - can't connect to db: ", $DBI::errstr;
+
+# generate output prefix name unless already specified
+$out = "${user}_stats" unless ($out);
+
+# find out the current month and year. Correct year to real 4-digit number.
+my ( $currDate, $currMon, $currYr ) = ( localtime() )[ 3 .. 5 ];
+$currYr += 1900;
+
+my $monthly = get_monthly($dbh);
+warn "Warning - no monthly data found\n" unless ( scalar @{$monthly} );
+my $daily = get_daily( $dbh, $currMon, $currYr );
+warn "Warning - no daily data found for $month[$currMon] $currYr\n" unless ( scalar @{$daily} );
+print_run_stats( $dbh, $runStats ) if ($runStats);
+$dbh->disconnect;
+
+if ($showPlot) {
+ print "Drawing plots...\n" unless ($quiet);
+ draw_graph( $monthly, 'Month', "Monthly Totals", "${out}_monthly.png" );
+ draw_graph( $daily, 'Date', "Daily Totals for $month[$currMon]", "${out}_daily.png" );
+}
+
+if ($showCSV) {
+ print "Writing CSV files...\n" unless ($quiet);
+ print_data( $daily, "${out}_daily.csv" );
+ print_data( $monthly, "${out}_monthly.csv" );
+}
+print "Finished!\n" unless ($quiet);
+exit;
+
+#########################################################################################################
+# count the number of jobs per month since records began
+sub get_monthly {
+ my $dbh = shift;
+
+ # retrieve all jobs run and give the epoch time they started.
+ # has a kludge to remove some extraneous run info for Aug 2008
+ my $sth = $dbh->prepare(
+ "SELECT EXTRACT(EPOCH FROM start_time) AS epoch
+ FROM view_accounting
+ WHERE username = '$user'
+ AND submission_time > '2008-sep-01'::Date
+ ORDER BY epoch ASC"
+ ) or die "ERROR - unable to prepare SELECT statement: ", $dbh->errstr();
+
+ $sth->execute();
+
+ # foreach epoch time retrieve month and year
+ # and count the number of jobs run per month
+ my %data;
+ while ( my @row = $sth->fetchrow_array ) {
+ my ( $mnth, $year ) = ( localtime( $row[0] ) )[ 4 .. 5 ];
+ $year += 1900;
+ $data{$year}{$mnth}++;
+ }
+
+ # convert month counts into data structure readable by GD::Graph
+ my $i = 0;
+ my @sortedData;
+ foreach my $year ( sort keys %data ) {
+ foreach my $mon ( sort { $a <=> $b } keys %{ $data{$year} } ) {
+ my $date = sprintf "%s %02d", $month[$mon], $year - 2000; # convert into 2-digit version (not Y2K compatible)
+ $sortedData[0][$i] = $date;
+ $sortedData[1][$i] = $data{$year}{$mon};
+ ++$i;
+ }
+ }
+ return ( \@sortedData );
+}
+
+#########################################################################################################
+# count the number of jobs per day of current month
+sub get_daily {
+ my $dbh = shift;
+ my $mnth = shift;
+ my $year = shift;
+
+ # retrieve the number of jobs run per day during this month
+ my $sth = $dbh->prepare(
+ "SELECT DISTINCT(CAST(start_time AS DATE)) AS start_date, COUNT(CAST(start_time AS DATE))
+ FROM view_accounting
+ WHERE username = '$user'
+ AND start_time >= '$year-$month[$mnth]-01'::Date
+ GROUP BY start_date
+ ORDER BY start_date ASC"
+ ) or die "ERROR - unable to prepare SELECT statement: ", $dbh->errstr();
+
+ $sth->execute();
+
+ # generate data structure for GD::Graph with day counts
+ my $i = 0;
+ my @data;
+ while ( my @row = $sth->fetchrow_array ) {
+ # $row[0] is the date
+ # $row[1] is the count
+ my $date = ( split( /-/, $row[0] ) )[2];
+
+ #print "$date: $row[1]\n";
+ $data[0][$i] = $date;
+ $data[1][$i] = $row[1];
+ ++$i;
+ }
+ $sth->finish();
+
+ return ( \@data );
+}
+
+#########################################################################################################
+# print out specific stats relating to run time, queuing time and exit status
+sub print_run_stats {
+ my ($dbh) = shift;
+ my $days = shift;
+
+ # get the date n days ago
+ my $secsInDays = 86400 * $days; # num seconds in a day * number of days
+ my $daysAgo = ( time() - $secsInDays );
+ my ( $date, $mnth, $year ) = ( localtime($daysAgo) )[ 3 .. 5 ];
+ $year += 1900;
+
+ #print "$days days ago was: $year-$month[$mnth]-$date\n";
+
+ # retrieve run-specific stats for the user
+ my $sth = $dbh->prepare(
+ "SELECT wallclock_time, maxvmem, exit_status, EXTRACT(EPOCH FROM start_time - submission_time) AS wait_time
+ FROM view_accounting
+ WHERE username = '$user'
+ AND submission_time >= '$year-$month[$mnth]-$date'::Date"
+ ) or die "ERROR - unable to prepare SELECT statement: ", $dbh->errstr();
+ $sth->execute() or die;
+ my $nRows = $sth->rows();
+
+ # open stats file
+ my $file = 'run_stats.csv';
+ open( my $OUT, ">>", $file ) or die "ERROR - unable to open '$file' for write: ${!}\nDied";
+ print $OUT "$currYr-$month[$currMon]-$currDate,$nRows,";
+
+ # if no jobs run in time frame warn, set everything to zero and return
+ if ( $nRows == 0 ) {
+ warn "Warning - no jobs found for user '$user' in the last $days days\n";
+ print $OUT "0,0,0,0,0\n";
+ close($OUT);
+ return;
+ }
+
+ # collate useful data
+ my %data;
+ while ( my @row = $sth->fetchrow_array ) {
+ $data{runtime} += $row[0];
+ $data{vmem} += $row[1];
+ if ( $row[2] > 0 ) {
+ if ( $row[2] == 4 ) {
+ $data{timeouts}++;
+ } else {
+ $data{errors}++;
+ }
+ }
+ $data{waittime} += $row[3];
+
+ }
+
+ # define potentially undefined variables
+ $data{timeouts} = 0 unless ( $data{timeouts} );
+ $data{errors} = 0 unless ( $data{errors} );
+
+ # write out data to file
+ foreach my $k qw(runtime vmem waittime) {
+ printf $OUT "%.0f,", $data{$k} / $nRows;
+ }
+ print $OUT "$data{timeouts},$data{errors}\n";
+}
+
+#########################################################################################################
+sub draw_graph {
+ my ( $dataref, $x_label, $title, $outFile ) = @_;
+
+ my $graph = GD::Graph::bars->new( 700, 400 );
+
+ $graph->set_title_font ( "$FONTPATH/VeraBd.ttf", 12 );
+ $graph->set_x_label_font ( "$FONTPATH/VeraBd.ttf", 8 );
+ $graph->set_y_label_font ( "$FONTPATH/VeraBd.ttf", 8 );
+ $graph->set_x_axis_font ( "$FONTPATH/Vera.ttf", 6 );
+ $graph->set_y_axis_font ( "$FONTPATH/Vera.ttf", 8 );
+ $graph->set(
+ x_label => $x_label,
+ y_label => 'No. Jpred Submissions',
+ title => $title,
+ shadow_depth => -2,
+ shadowclr => 'lgray',
+ x_labels_vertical => 1,
+
+ # borderclrs => undef,
+ bar_width => 12,
+ bar_spacing => 4
+ ) or die $graph->error;
+
+ my $gd = $graph->plot($dataref) or die $graph->error;
+
+ open( my $IMG, ">", $outFile ) or die "ERROR - unable to open '$outFile' for write: ${!}\nDied";
+ binmode $IMG;
+ print $IMG $gd->png;
+ close($IMG);
+
+}
+
+#########################################################################################################
+sub print_data {
+ my $data = shift;
+ my $file = shift;
+
+ if ( !scalar @{$data} ) {
+ warn "Warning - no data to print out. Nothing to do.\n";
+ return;
+ }
+
+ my $total = scalar @{ $data->[0] };
+
+ open( my $OUT, ">", $file ) or die "ERROR - unable to open '$file' for write: ${!}\nDied";
+ print $OUT "Date,nRuns\n";
+ for ( my $i = 0 ; $i < $total ; ++$i ) {
+ print $OUT "$data->[0][$i],$data->[1][$i]\n";
+ }
+}
+
+#########################################################################################################
+=head1 SYNOPSIS
+
+arco_stats.pl --user <sge_user> [--out <file_prefix> --x <pixels> --y <pixels>] [--csv] [--plot] [--run-stats <days>] [--quiet] [--man] [--help]
+
+=head1 DESCRIPTION
+
+Script to collate run statistics from the SGE ARCo system.
+
+The script will retrieve all historical data for the specified, count the number of jobs run and collate them by month. For the current month, data will be broken down by day.
+
+With no options script will get stats for the www-jpred user and output CSV formatted data only. Filenames will take the form <username>_stats_[daily|monthly].csv, unless specified with the --out switch.
+
+=head1 OPTIONS
+
+=over 5
+
+=item B<--user>
+
+Specify SGE user. [Default: www-jpred]
+
+=item B<--out>
+
+Ouput filename prefix.
+
+=item B<--x>
+
+Specific X-dimension of plot figure in pixels. [Default: 700]
+
+=item B<--y>
+
+Specific Y-dimension of plot figure in pixels. [Default: 400]
+
+=item B<--csv>,B<--nocsv>
+
+Toggle for CSV output. [Default: on]
+
+=item B<--plot>,B<--noplot>
+
+Toggle for plotting of data. [Default: off]
+
+=item B<--run-stats>
+
+Set the number of days for collating run statistics (e.g. mean run time, mean wait time). [Default: 0]
+
+=item B<--quiet>
+
+Switch off progress messages. Useful if running in cron.
+
+=item B<--help>
+
+Brief help.
+
+=item B<--man>
+
+Full manpage of program.
+
+=back
+
+=head1 BUGS
+
+Script assumes it won't run in the past and threfore is not Y2K compliant.
+
+=head1 AUTHOR
+
+Chris Cole <christian@cole.name>
+
+=cut
--- /dev/null
+#!/usr/bin/perl
+
+# Generates PS from a blc file (generally made by concise2blc)
+
+use strict;
+use warnings;
+use Getopt::Long;
+
+use Jpred;
+
+my ($in, $out, $ps);
+GetOptions(
+ "in=s" => \$in,
+ "out=s" => \$out,
+ "postscript=s" => \$ps
+);
+
+die "No input BLC file given\n" unless defined $in;
+die "No output path given\n" unless defined $out;
+die "No PostScript output path given\n" unless defined $ps;
+
+#xsystem("$BINDIR/prettify -f $in -prefix $out -ignore 2");
+xsystem("$BINDIR/prettify.pl --blc $in --alscript $out --postscript $ps");
+xsystem("$BINDIR/alscript -f $out");
--- /dev/null
+#!/usr/bin/perl
+
+#
+# Generates a blc file from the concise file, reads in the sequence
+# alignments those records in @data
+#
+
+#
+# CC 22/06/07 - bug fix in 'conversion' of coil-coiled predictions
+# CC 22/05/06 - bug fix in final foreach loop
+#
+
+use strict;
+use warnings;
+
+if ($ARGV[0]) { open(IN, "<$ARGV[0]") or die($!); }
+else { open(IN, "<-") or die($!); }
+
+# The names of the records from the concise file that we want
+my @data = ("JNETALIGN", "JNETHMM", "jnetpred", "JNETPSSM", "JNETCONF", "JNETSOL25", "JNETSOL5", "JNETSOL0", "Lupas_21", "Lupas_14", "Lupas_28");
+
+my %convert = ("JNETALIGN" => "jalign",
+ "JNETHMM" => "jhmm",
+ "jnetpred" => "jnet",
+ "JNETPSSM" => "jpssm",
+ "JNETCONF" => "conf",
+ "JNETSOL25" => "sol25",
+ "JNETSOL5" => "sol5",
+ "JNETSOL0" => "sol0",
+ "Lupas_21" => "lupas_21",
+ "Lupas_14" => "lupas_14",
+ "Lupas_28" => "lupas_28",
+ );
+
+my (@seq, %seq, @pred, %pred); # CC - these could be replaced with a tied hash, for future edits.
+
+#
+# Read in the concise file and extract the data
+#
+
+while (<IN>) {
+ if (/^\n/) { next; }
+ my ($id, $seq) = split(":", $_);
+ if (!$id || !$seq) { next; } # Check we have proper values
+ chomp($seq);
+ $seq =~ s/,//g;
+ if ($id =~ /align\d*;/) {
+ @_ = split(";", $id); # Then its an alignment
+ push @seq, $_[1];
+ $seq{$_[1]} = $seq;
+ }
+ foreach (@data) {
+ if ($id eq $_) {
+ push @pred, $_;
+ $pred{$_} = $seq;
+ }
+ }
+ }
+close(IN);
+
+my @blc;
+my $gap;
+my $seq_len = length($seq{$seq[0]}) - 1;
+foreach (0..$seq_len) { $gap .= " "; }
+
+push @blc, $gap;
+
+foreach (@seq) {
+ $seq{$_} =~ s/\.|-/ /g;
+ push @blc, $seq{$_};
+ }
+push @blc, $gap;
+push @blc, $gap;
+push @blc, $gap;
+foreach (@pred) {
+ ## CC 22/06/07 - Convert 8-state secondary structure types to 3-state types unless
+ ## it's a coil-coil prediction where 'C' is a valid prediction.
+ ## I think this is a throw-back from when Jpred was a consensus server?
+ if ($_ =~ /Lupas/i) {
+ $pred{$_} =~ s/-/ /g;
+ } else {
+ $pred{$_} =~ s/[TCYWXZ_SI\?-]/ /g;
+ $pred{$_} =~ s/G/H/g;
+ }
+ push @blc, $pred{$_};
+}
+
+foreach (@seq) {
+ print ">$_\n";
+ }
+print ">\n>\n>\n";
+foreach (@pred) {
+ print ">$convert{$_}\n";
+ }
+print " * iteration 1\n";
+#print " $seq_len\n";
+
+foreach my $i (0..$seq_len) {
+ foreach (@blc) {
+ ### CC 22/05/06 - below has been changed due to bug where if
+ # statement return false when $b == 0. This should actually
+ # be true when parsing the JNETCONF string of integers.
+ #
+ # Now we test whether the variable is defined rather than true.
+ # NB: not sure what do if the variable is not defined?
+
+ #if (my $b = substr($_, $i, 1)) { print $b; }
+
+ my $value = substr($_, $i, 1);
+ print $value if defined($value);
+ }
+ print "\n";
+ }
+print " *";
--- /dev/null
+#!/usr/bin/perl
+
+# Converts concise file into fasta format
+# also puts in the consensus.
+
+use strict;
+use warnings;
+
+my ( @seqs, %seq, @pred, %pred );
+
+my @var = (
+ "Lupas_21", "Lupas_14", "Lupas_28", "JNETPSSM", "MULTCOIL", "MULTCOIL_TRIMER", "MULTCOIL_DIMER", "JNETFREQ",
+ "JNETALIGN", "JNETHMM", "JNETSOL5", "JNETSOL25", "JNETSOL0", "jnetpred", "jpred", "JNETCONF"
+);
+
+if ( $ARGV[0] ) { open( IN, "<$ARGV[0]" ) or die($!); }
+else { open( IN, "<-" ) or die($!); }
+
+while (<IN>) {
+ if (/^\n/) { next; }
+ my ( $id, $seq ) = split( ":", $_ );
+ if ( !$id || !$seq ) { next; } # Check we have proper values
+ $seq =~ s/,//g;
+ chomp($seq);
+ if ( $id =~ /;/ ) { # Then it's an alignment
+ @_ = split( ";", $id );
+ push @seqs, $_[1];
+ $seq{ $_[1] } = $seq;
+ }
+ foreach (@var) {
+ if ( $_ eq $id ) {
+ push @pred, $_;
+ $pred{$_} = $seq;
+ }
+ }
+}
+close(IN);
+
+foreach (@seqs) {
+ $seq{$_} =~ s/(.{72})/$1\n/g;
+ print ">$_\n$seq{$_}\n";
+}
+
+foreach (@pred) {
+ $pred{$_} =~ s/[TCYWXZSI\?_]/-/g;
+ $pred{$_} =~ s/B/E/g;
+ $pred{$_} =~ s/G/H/g;
+
+ if (/SOL/) { $pred{$_} =~ s/E/B/g; }
+ $pred{$_} =~ s/(.{72})/$1\n/g;
+ print ">$_\n$pred{$_}\n";
+}
--- /dev/null
+#!/usr/bin/perl
+
+use strict;
+use warnings;
+use Jpred;
+use Getopt::Long;
+
+my ($in, $out);
+my $format = 'seq';
+GetOptions(
+ "in=s" => \$in,
+ "out=s" => \$out,
+ "format=s" => \$format
+);
+
+if (!$in) { $in = "-"; }
+if (!$out) { $out = "-"; }
+
+# Read in the concise CSV file. Data is stored in hash's with the key
+# being the name of the type of data and the value being the sequence
+# data, the order of the alignments is also stored for display in the
+# order with which they are aligned.
+
+my (@align, @seq, %predict, %prob);
+
+my @predictions = qw(Lupas_14 Lupas_21 Lupas_28 jnetpred JNETHMM JNETALIGN JNETPSSM JNETJURY JNETSOL25 JNETSOL5 JNETSOL0 JNETCONF);
+
+my @prob = qw(JNETPROPH JNETPROPB JNETPROPC);
+
+# Arrays that holds the order in which things are printed
+my @print_pred = qw(jnetpred JNETALIGN JNETHMM JNETPSSM);
+my @coils = qw(Lupas_14 Lupas_21 Lupas_28);
+my @solvent = qw(JNETSOL25 JNETSOL5 JNETSOL0);
+
+# Hash that relates data names to printed names
+my %convert = (
+ JNETALIGN => "jalign",
+ JNETHMM => "jhmm",
+ jnetpred => "Jnet",
+ JNETPSSM => "jpssm",
+
+ Lupas_14 => "Lupas 14",
+ Lupas_21 => "Lupas 21",
+ Lupas_28 => "Lupas 28",
+
+ JNETSOL25 => "Jnet_25",
+ JNETSOL5 => "Jnet_5",
+ JNETSOL0 => "Jnet_0",
+ JNETCONF => "Jnet Rel"
+);
+
+# Read in the data
+open(IN, "<$in") or die($!);
+while (<IN>) {
+ if (/:/) {
+ my ($id, $seq) = split(":", $_);
+
+ if ($id =~ /;/) { # Find sequence alignments
+ my ($align, $seqid) = split(";", $id);
+ push @align, $seqid;
+ $seq =~ s/,//g;
+ chomp($seq);
+ push @seq, $seq;
+ }
+
+ foreach (@predictions) { # Find the predictions
+ if ($id eq $_) {
+ if ($predict{$id}) { die("Same ID ($id) found twice in concise file!"); }
+ $seq =~ s/,//g;
+ chomp($seq);
+ $predict{$id} = $seq;
+ }
+ }
+
+ foreach (@prob) {
+ if ($id eq $_) {
+ if ($prob{$id}) { die("Same ID ($id) found twice in concise file!"); }
+ chomp($seq);
+ @_ = split(",", $seq);
+ foreach (@_) {
+ if ($_ >= 0.85) { $_ = 9; }
+ else { $_ = int(($_ * 10) + 0.5); }
+ }
+ my $temp = join("", @_);
+ $prob{$id} = $temp;
+ }
+ }
+ }
+ }
+close(IN);
+
+############################################
+#
+# Sets up the references for prediction
+# methods and deffn methods
+#
+
+my @predname = qw(jnetpred JNETALIGN JNETPSSM JNETHMM);
+foreach (@predname) {
+ if (!$predict{$_}) { warn("\"$_\" data not present\n"); next; }
+ $predict{$_} =~ s/[TCYWXZ]/-/g;
+ }
+
+######################################################################
+# Print out the sequences to HTML
+######################################################################
+
+open(HTML, ">$out") or die($!);
+print HTML "<!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 3.2//EN\"><html><head><meta http-equiv=\"Content-Type\" content=\"text/html; charset=iso-8859-1\"><title>Jpred secondary structure prediction results</title></head><body bgcolor=\"#ffffff\"><pre><code>";
+
+#
+# Prints the sequence passed to it as a reference to an array, second
+# array contains the "conservation", which varies between 0 and 1 for
+# each position.
+#
+
+sub printseq {
+ my $seqref = shift @_;
+ my $scoreref = shift @_;
+
+ unless ($scoreref) {
+ foreach (0..$#{$seqref}) {
+ print HTML ${$seqref}[$_];
+ }
+ return;
+ }
+
+# foreach (0..$#{$seqref} - 1) {
+ foreach (0..$#{$seqref}) {
+ my $colour = "#"; # Work out the colour
+ if (${$scoreref}[$_] == 1) {
+ $colour .= "0000ff";
+ }
+ else {
+ $colour .= (sprintf "%-2.2lx", ${$scoreref}[$_] * 255).(sprintf "%-2.2lx", 0).(sprintf "%-2.2lx", 0);
+ }
+
+ print HTML "<font color=\"$colour\">${$seqref}[$_]</font>";
+ }
+}
+
+# Prints the gap at the begining of the line between the sequence ID
+# and the ":". First argument is the length of the ID and the second is
+# the maximimum length.
+
+sub printgap {
+ my ($strlen, $max_len) = @_;
+ foreach ($strlen .. $max_len) {
+ print HTML " ";
+ }
+ print HTML ": ";
+ }
+
+# Works out a consensus score according to Zvelebil et al. (1987)
+# J. Mol. Biol. 195, pp957, and does the smoothing
+
+sub cons {
+ my %conservation = (
+ I => [1, 0, 0, 0, 0, 0, 0, 1, 0, 0],
+ L => [1, 0, 0, 0, 0, 0, 0, 1, 0, 0],
+ V => [1, 0, 0, 0, 0, 1, 0, 1, 0, 0],
+ C => [1, 0, 0, 0, 0, 1, 0, 0, 0, 0],
+ A => [1, 0, 0, 0, 0, 1, 1, 0, 0, 0],
+ G => [1, 0, 0, 0, 0, 1, 1, 0, 0, 0],
+ M => [1, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+ F => [1, 0, 0, 0, 0, 0, 0, 0, 1, 0],
+ Y => [1, 0, 0, 1, 0, 0, 0, 0, 1, 0],
+ W => [1, 0, 0, 1, 0, 0, 0, 0, 1, 0],
+ H => [1, 1, 0, 1, 1, 0, 0, 0, 1, 0],
+ K => [1, 1, 0, 1, 1, 0, 0, 0, 0, 0],
+ R => [0, 1, 0, 1, 1, 0, 0, 0, 0, 0],
+ E => [0, 0, 1, 1, 0, 0, 0, 0, 0, 0],
+ Q => [0, 0, 0, 1, 1, 0, 0, 0, 0, 0],
+ D => [0, 0, 1, 1, 0, 1, 0, 0, 0, 0],
+ N => [0, 0, 0, 1, 0, 1, 0, 0, 0, 0],
+ S => [0, 0, 0, 1, 0, 1, 1, 0, 0, 0],
+ T => [1, 0, 0, 1, 0, 1, 0, 0, 0, 0],
+ P => [0, 0, 0, 0, 0, 1, 0, 0, 0, 1],
+ Z => [0, 0, 0, 1, 0, 0, 0, 0, 0, 0],
+ '-' => [1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
+ '_' => [1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
+ '.' => [1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
+ X => [1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
+ B => [1, 1, 1, 1, 1, 1, 1, 1, 1, 1], # Not mentioned, so use X
+ U => [1, 0, 0, 0, 0, 1, 0, 0, 0, 0], # Not mentioned, so use C
+ );
+
+ my $aref = shift @_;
+ my (@cons, @align);
+
+ # Get each sequence
+ foreach (@{$aref}) {
+ push @align, $_;
+ }
+
+ my $seq_len = length($align[0]);
+
+ # Foreach position
+ foreach my $pos (0..$seq_len - 1) {
+ my @temp;
+
+ # Foreach sequence, get the residue for this position
+ foreach (@align) { push @temp, substr($_, $pos, 1); }
+
+ my ($p, $i, $j);
+ for ($i = 0; $i < $#temp; $i++) {
+ my $one = uc($temp[$i]);
+ for ($j = $i + 1; $j < $#temp; $j++) {
+ my $two = uc($temp[$j]);
+ foreach (0..9) {
+ # This debugging is in here
+ # incase a residue occurs that we
+ # haven't got in the hash above
+ unless (defined $conservation{$one}[$_]) {
+# warn "first $one, $_\n";
+# die "'$conservation{$one}[$_]'\n";
+ next;
+ }
+ unless (defined $conservation{$two}[$_]) {
+# warn "second $two, $_\n";
+# die "'$conservation{$two}[$_]'\n";
+ next;
+ }
+ if ($conservation{$one}[$_] != $conservation{$two}[$_]) { $p++; }
+ }
+ }
+ }
+
+ # This loop looks to be v. slow
+ if ($p) {
+ if (($p = 0.9 - 0.1 * $p) < 0) { $p = 0; }
+ }
+ else {
+ for ($i = 1; $i < $#temp; $i++) {
+ if ($temp[$i] ne $temp[0]) {
+ $p++;
+ last;
+ }
+ }
+ if ($p) { $p = 0.9; }
+ else { $p = 1; }
+ }
+
+ push @cons, $p;
+ }
+
+ # Average the result over 3 residues
+# my (@final, $i);
+# push @final, $cons[0];
+# for ($i = 1; $i < ($#cons); $i++) {
+# push @final, ($cons[$i - 1] + $cons[$i] + $cons[$i + 1]) / 3;
+# }
+# push @final, $cons[$#cons + 1];
+
+ return @cons;
+}
+
+############################################################
+# Uncomment this to get the conservation scoring worked out
+############################################################
+#my @score = &cons(\@seq);
+
+#
+# Print the sequences
+#
+
+# Find the longest identifier and set the space at the start of the line
+
+my $max_len = 0;
+foreach (@align) {
+ if (length($_) > $max_len) { $max_len = length($_); }
+ }
+if ($max_len <= 6) { $max_len = 11; }
+
+foreach (0..$#align) {
+ # Begining of line
+ if ($_ == 0) {
+ print HTML "$align[$_]";
+ }
+ else {
+ if ($format eq 'seq') {
+ ## differentiate between Uniprot and Uniparc (UniRef90_UNI\w+) IDs as they require
+ ## different SRS query strings
+ if ($align[$_] =~ /UniRef90_(UPI\w+)/) {
+ print HTML "<a href=$SRSSERVER/wgetz?-e+[uniparc-AccNumber:$1]>$align[$_]</a>";
+ } else {
+ print HTML "<a href=$SRSSERVER/wgetz?-e+[UNIREF90-acc:$align[$_]]>$align[$_]</a>";
+ }
+ } else {
+ print HTML "$align[$_]";
+ }
+ }
+ &printgap(length($align[$_]) ,$max_len);
+
+ # Print the sequence
+ @_ = split("", $seq[$_] );
+# &printseq([@_], [@score]);
+ &printseq([@_]);
+
+ # End of the line
+ if ($_ == 0) {
+ print HTML " : $align[$_] \n";
+ }
+ else {
+ if ($format eq 'seq') {
+ ## differentiate between Uniprot and Uniparc IDs as they require
+ ## different SRS query strings
+ if ($align[$_] =~ /UniRef90_(UPI\w+)/) {
+ print HTML " : <a href=$SRSSERVER/wgetz?-e+[uniparc-AccNumber:$1]>$align[$_]</a>\n";
+ } else {
+ print HTML " : <a href=$SRSSERVER/wgetz?-e+[UNIREF90-acc:$align[$_]]>$align[$_]</a>\n";
+ }
+ } else {
+ print HTML " : $align[$_]\n";
+ }
+ }
+ }
+print HTML "\n";
+
+######################################################################
+
+#
+# Create a guide sequence of the original query
+# (of the form 1----------11--- etc.)
+#
+
+my ($guide, $i);
+my $seq_len = length($seq[0]);
+
+for ($i = 1; $i < $seq_len; $i += 10) {
+ my $dash;
+ my $no_dash = 9 - length($i);
+ foreach (0..$no_dash) { $dash .= "-"; }
+ $guide .= $i.$dash;
+ }
+
+while (length($guide) > $seq_len) { # Trim spare guide away
+ chop($guide);
+ }
+
+printgap(0, $max_len);
+print HTML $guide." :\n";
+
+print HTML "OrigSeq";
+printgap(7, $max_len);
+print HTML $seq[0];
+print HTML " : OrigSeq\n\n";
+
+# Print out secondary structure predictions, goes through in order of
+# @print_pred so comes out right
+
+foreach (@print_pred) {
+ if (!$predict{$_}) { next; }
+ if ($_ eq "JNETALIGN") { # Add a line before JNETALIGN which will put jnetpred on its own
+ print HTML "\n";
+ }
+
+ print HTML $convert{$_};
+ printgap(length($convert{$_}), $max_len);
+ @_ = split("", $predict{$_});
+ foreach (@_) {
+ if ($_ eq "E") {
+ print HTML "<font color=ffa800>$_</font>";
+ }
+ elsif ($_ eq "H") {
+ print HTML "<font color=e90055>$_</font>";
+ }
+ elsif ($_ eq "-") {
+ print HTML $_;
+ }
+ }
+ print HTML " : $convert{$_}\n";
+ }
+print HTML "\n";
+
+foreach (@coils) {
+ if (!$predict{$_}) { next; }
+ print HTML $convert{$_};
+ printgap(length($convert{$_}), $max_len);
+ @_ = split("", $predict{$_});
+ foreach (@_) {
+ if ($_ eq "C") { print HTML "<font color=00aa00>$_</font>"; }
+ else { print HTML $_; }
+ }
+ print HTML " : $convert{$_}\n";
+ }
+print HTML "\n";
+
+foreach (@solvent) {
+ if (!$predict{$_}) { next; }
+ print HTML $convert{$_};
+ printgap(length($convert{$_}), $max_len);
+ @_ = split("", $predict{$_});
+ foreach (@_) {
+ if ($_ eq "B") {
+ print HTML "<font color=aa0000>$_</font>";
+ }
+ else { print HTML $_; }
+ }
+ print HTML " : $convert{$_}\n";
+ }
+
+printf HTML $convert{"JNETCONF"};
+printgap(8, $max_len);
+
+@_ = split("", $predict{"JNETCONF"});
+foreach (@_) {
+ if ($_ >= 7) { print HTML "<font color=00aa00>$_</font>"; }
+ else { print HTML "$_"; }
+ }
+print HTML " : ".$convert{"JNETCONF"}."\n";
+
+print HTML "</code></pre>";
+print HTML "<hr>";
+
+#
+# Key to data
+#
+
+print HTML "<pre><code>";
+print HTML "<b>\nNotes
+Key:</b>
+Colour code for alignment:
+Blue - Complete identity at a position
+Shades of red - The more red a position is, the higher the level of
+ conservation of chemical properties of the amino acids
+Jnet - Final secondary structure prediction for query
+jalign - Jnet alignment prediction
+jhmm - Jnet hmm profile prediction
+jpssm - Jnet PSIBLAST pssm profile prediction
+
+Lupas - Lupas Coil prediction (window size of 14, 21 and 28)
+
+Note on coiled coil predictions - = less than 50% probability
+ c = between 50% and 90% probability
+ C = greater than 90% probability
+
+Jnet_25 - Jnet prediction of burial, less than 25% solvent accesibility
+Jnet_5 - Jnet prediction of burial, less than 5% exposure
+Jnet_0 - Jnet prediction of burial, 0% exposure
+Jnet Rel - Jnet reliability of prediction accuracy, ranges from 0 to 9, bigger is better.
+";
+
+print HTML "</code></pre>$JPREDFOOT</body></html>";
+close(HTML);
--- /dev/null
+#! /usr/bin/perl
+
+use strict;
+use warnings;
+
+use lib '/homes/www-jpred/new_site/jpred_new/lib';
+
+use Concise;
+use Concise::File;
+
+use Getopt::Long;
+use Pod::Usage;
+
+my $file;
+my $out;
+my $help;
+my $man;
+
+GetOptions (
+ 'file=s' => \$file,
+ 'out=s' => \$out,
+ 'help|?' => \$help,
+ 'man' => \$man
+) or pod2usage(0);
+
+pod2usage(-verbose => 1) if $help;
+pod2usage(-verbose => 2) if $man;
+pod2usage(-msg => 'Please give a concise file to read', -verbose => 0) if (!$file);
+
+## Hash of description lines for concise data types
+my %desc = (
+ jnetpred => 'Final secondary structure prediction by Jnet',
+ JNETHMM => 'Jnet prediction using HMMer profiles',
+ JNETPSSM => 'Jnet prediction using PSSM profiles',
+ JNETJURY => 'Positions where Jnet predictions do not agree',
+ JNETSOL0 => 'Jnet solvent relative accessibility prediction at 0% cut-off',
+ JNETSOL5 => 'Jnet solvent relative accessibility prediction at 5% cut-off',
+ JNETSOL25 => 'Jnet solvent relative accessibility prediction at 25% cut-off',
+ JNETCONF => 'Confidence of Jnet prediction 0 (low) -> 9 (high)',
+ Lupas_14 => 'Coiled-coil prediction windowed over 14 residues',
+ Lupas_21 => 'Coiled-coil prediction windowed over 21 residues',
+ Lupas_28 => 'Coiled-coil prediction windowed over 28 residues',
+);
+
+## If an output file is given open it and select it as the default output
+my $FH;
+if ($out) {
+ open($FH, ">$out") or die "ERROR - unable to open '$out' for writing: $!\nDied";
+ select($FH);
+}
+
+## Create a Concise::File object and fill it with the contents of the input file
+my $concise = Concise::File->new(read_file => $file);
+
+## Write the Jalview Annotation file to the default output
+print "JALVIEW_ANNOTATION\n";
+print "# Created by concise2jalview using '$file' as input\n\n";
+for my $data ($concise->get_entries) {
+ my $string = join("|", $data->seq);
+ if ($data->id =~ /prop|align/i) { # skip sequence alignments and PROPH|C|E fields
+ next;
+ } elsif ($data->id =~ /jnetconf/i) { # treat Jnet confidence as a bar graph as contains real numbers
+ print "BAR_GRAPH\t", $data->id,"\t",$desc{$data->id}, "\t$string\n";
+ next;
+ } elsif ($data->id =~ /jnet(pred|hmm|align|pssm)/i) { # strip out '-' chars from prediction fields as unrequired by Jalview
+ $string =~ s/-//g;
+ }
+ # By default don't treat fields as graphable data and add a description line
+ print "NO_GRAPH\t",$data->id,"\t",$desc{$data->id}, "\t$string\n";
+}
+exit;
+
+=head1 NAME
+
+concise2jalview -- covert Jnet concise files to Jalview annotation files
+
+=head1 SYNOPSIS
+
+concise2jalview --file <concise file> [--help] [--man] > <output file>
+
+=head1 DESCRIPTION
+
+This script takes a Jnet concise file as input and returns a Jalview annotation file as output. This allows Jalview to better view Jnet/Jpred prediction complete with descriptions of the various predictions.
+
+All data types are included in the Jalview file except for 'JNETPROP*' and any sequence alignments.
+
+=head1 OPTIONS
+
+=over 4
+
+=item B<--file> <concise file>
+
+Give the path and name to the Jnet concise file.
+
+=item B<--help>
+
+Displays brief help.
+
+=item B<--man>
+
+Displays the full manpage.
+
+=back
+
+=head1 AUTHOR
+
+Chris Cole <christian@cole.name>
+
+=cut
--- /dev/null
+#!/usr/bin/perl
+
+## CC 18/05/2006
+# New version of script as the original (OO perl) version
+# doesn't work on the new cluster. As it's a very simple
+# parser it can be easily re-implemented
+
+use strict;
+use warnings;
+use Getopt::Long;
+use Jpred;
+
+my $file;
+my $out;
+
+GetOptions(
+ 'file=s' => \$file,
+ 'out=s' => \$out
+) or die $!;
+
+$file or die "no --file argument\n";
+
+open(my $FH, $file) or die "$!";
+my $query;
+my $pred;
+while(<$FH>) {
+ # jnet concise file is a series of outputs preceeded by
+ # a definition separated by ':' on each line e.g.:
+ #
+ # align1;QUERY:M,F,L,A,Q,E,I,I,R,K,K,R,D,G,H,A,L,S,D,E,E,I,...,
+ # jpred:-,-,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,H,H,H,H,H,H,H,...,
+ #
+ # Find the two lines above and extract the query sequence and the
+ # jpred prediction.
+
+ chomp;
+
+ my ($def, $data) = split /:/, $_ or next;
+
+ if ($def eq 'jnetpred') {
+ $pred = $data;
+ $pred =~ s/\,//g; # remove all the ',' in prediction
+ }
+ if ($def =~ /align1/) {
+ next if $query; # skip any hits to align1x sequences. We only want the 1st hit.
+ $query = $data;
+ $query =~ s/\,//g; # remove all ',' in sequence
+ }
+}
+close($FH);
+if (!$query || !$pred) {
+ die "no jpred output or query sequence found in $file";
+}
+
+# colour the predictions
+$pred =~ s{([H]+)}{<font color="#e90055">$1</font>}g;
+$pred =~ s{([E]+)}{<font color="#ffa800">$1</font>}g;
+
+if ($out) {
+ open(my $OUT, ">$out") or die "$out: $!";
+ select($OUT);
+}
+
+
+my $html = '<?xml version="1.0" encoding="iso-8859-1"?>
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html lang="en-GB" xml:lang="en-GB">
+<head><title>Simple JNet Output</title>
+<link rel="stylesheet" type="text/css" href="http:/webservices:12345/jpred.css" />
+</head><body><pre><code>';
+$html .= "$query\n";
+$html .= "$pred\n";
+$html .= "</code></pre>
+$JPREDFOOT</body></html>";
+print $html;
+
+exit;
+
--- /dev/null
+#!/usr/bin/perl
+
+# Script to create README file, run in the directory with the results in it.
+# Outputs to STDOUT by default, change with --out option or redirect.
+# If you're using an alignment give the --format msf option
+
+use strict;
+use warnings;
+use Getopt::Long;
+
+my ($out, $format);
+GetOptions(
+ "o|out=s" => \$out,
+);
+
+$out = '-' unless $out;
+
+## create look-up table of descriptions for files created by Jpred
+my %file = (
+ 'LOG' => "The log file of the prediction\n",
+ 'README' => "This file\n",
+ '.align' => "PSIBLAST alignment with gaps and redundancy removed in FASTA format\n",
+ '.align.msf' => "Your alignment in MSF format\n",
+ '.als' => "Alscript command file. Used to generate PS/PDF output",
+ '.blast.gz' => "PSIBLAST output (compressed)\n",
+ '.coils.csv' => "The output from coils in CSV format\n",
+ '.coilseq.lupas_14' => "The output from coils using a window length of 14\n",
+ '.coilseq.lupas_21' => "The output from coils using a window length of 21\n",
+ '.coilseq.lupas_28' => "The output from coils using a window length of 28\n",
+ '.concise' => "The prediction in pseudo-CSV format, including the coiled-coil prediction, solvent accessiblity and the sequence alignment\n",
+ '.concise.blc' => "A BLC file of the prediction and alignment\n",
+ '.concise.pdf' => "A PDF file of the prediction and alignment\n",
+ '.concise.ps' => "A PostScript file of the prediction and alignment\n",
+ '.fasta' => "Input query sequence in FASTA format\n",
+ '.hmm' => "The HHMer2 profile of the alignment\n",
+ '.html' => "A HTML file of the prediction and alignment\n",
+ '.input' => "Your raw input\n",
+ '.jalview' => "A Jalview annotation file to be read in with the .align file to view the predictions in Jalview\n",
+ '.jnet' => "The output from Jnet\n",
+ '.profile' => "PSIBLAST profile\n",
+ '.pssm' => "PSIBLAST PSSM in a format for Jnet\n",
+ '.seq' => "Your sequence\n",
+ '.simple.html' => "The brief HTML output of the query sequence and prediction only\n",
+ '.tar.gz' => "An archive of all the files in the directory\n",
+);
+
+## open the current directory
+opendir DIR, $ENV{'PWD'} or die "$ENV{PWD}: $!\n";
+
+## find the longest filename in order to correctly format the file
+my $len = 0;
+foreach (readdir DIR) { $len = length if length > $len; }
+rewinddir DIR;
+$len = "%-".($len + 5)."s%s"; # filename format for printing is max. length + 5 chars
+
+## Open output and write formatted filenames with their descriptions
+open FILE, ">$out" or die "$out: $!\n";
+printf FILE $len, "Filename", "Description\n";
+printf FILE $len, "--------", "-----------\n";
+
+foreach my $file (sort readdir DIR) {
+ # determine the extension for each file
+ my ($extn) = ($file =~ /[^.]*(.*)$/);
+
+ # remove unwanted files - Alignment in CSV format (can be found in the .concise file)
+ # and the SGE job files
+ unlink $file if ($extn eq '.align.csv');
+ unlink $file if ($extn =~ /\.[eo]\d{6}$/);
+
+ # output the formatted filename along with its description if it has a known extension
+ printf FILE $len, $file, $file{$extn} if $file{$extn};
+}
+close(FILE);
+exit;
+
--- /dev/null
+58 23 * * * cd /homes/www-jpred/live/public_html/stats && /homes/www-jpred/live/bin/arco_stats.pl --out jpred --plot --run-stats 14 --quiet || mail -s "Jpred stats have errors" www-jpred@compbio.dundee.ac.uk
+00 01 * * Sat rm -f /cluster/gjb_lab/fc/www-jpred/results/*.host
+00 05 * * * find /cluster/gjb_lab/fc/www-jpred/results -mtime +3 -type d -maxdepth 1 -name "jp_*" -exec rm -rf {} \;
+02 00 * * * rm -f /cluster/gjb_lab/fc/www-jpred/results/daily_count/*
--- /dev/null
+#!/usr/bin/perl
+
+#
+# Removes insertions (represented by "-" or ".") from FASTA files
+#
+
+use strict;
+use warnings;
+
+if ($ARGV[0]) { open(FILE, "<$ARGV[0]") or die($!); }
+else { open(FILE, "<-") or die($!); }
+
+my $seq;
+
+while (<FILE>) {
+ if (! /^>/) {
+ s/-|\.|\n//g;
+ $seq .= $_;
+ }
+ else { # If there's a sequence print it
+ if ($seq) { $seq =~ s/(.{72})/$1\n/g; print "$seq\n"; }
+ print $_; # Then the title
+ $seq = "";
+ }
+ }
+if ($seq) { $seq =~ s/(.{72})/$1\n/g; print "$seq\n"; }
--- /dev/null
+#!/usr/bin/perl
+
+# Converts a FASTA alignment of *sequences* to a concise file of the
+# form alignX;seq name:seq where X is an incremental integer and seq is
+# a comma seperated list of the sequence
+
+use warnings;
+
+if ( $ARGV[0] ) { open( IN, "<$ARGV[0]" ) or die($!); }
+else { *IN = *STDIN; }
+
+my ( $seq, @seqs, @title );
+while (<IN>) {
+ if (s/^>//) {
+ if ($seq) {
+ $seq =~ s/\n|\s//g;
+ $seq =~ s/(.)/$1,/g;
+ push @seqs, $seq;
+ $seq = "";
+ }
+ chomp;
+ push @title, $_;
+ } else {
+ chomp;
+ $seq .= $_;
+ }
+}
+$seq =~ s/\n|\s//g;
+$seq =~ s/(.)/$1,/g;
+push @seqs, $seq;
+
+if ( @title != @seqs ) { die("non matching number of titles and sequences!\n"); }
+
+foreach ( 0 .. $#title ) {
+ print "align" . ( $_ + 1 ) . ";$title[$_]:$seqs[$_]\n";
+}
--- /dev/null
+#!/usr/bin/perl
+
+#
+# Returns the first sequence from a FASTA file
+#
+
+use warnings;
+
+if ($ARGV[0]) { open(IN, "<$ARGV[0]") or die($!); }
+else { *IN = *STDIN; }
+
+while (<IN>) {
+ if (/^>/) {
+ print $_;
+ while (<IN>) {
+ if (/^>/) { exit(); }
+ print $_;
+ }
+ }
+ }
--- /dev/null
+#!/usr/bin/perl
+
+=head1 NAME
+
+jpred_stats.pl - Collate Monthly and Daily usage statistics for the Jpred server
+
+=cut
+
+use strict;
+use warnings;
+use GD::Graph::bars;
+use Getopt::Long;
+use Pod::Usage;
+
+# path for nicer fonts for the graph labels
+my $FONTPATH = "$ENV{HOME}/bin/fonts/";
+
+my $help;
+my $man;
+my $outPath = '.';
+my $file = '/grid/default/common/accounting';
+
+GetOptions(
+ 'source=s' => \$file,
+ 'path=s' => \$outPath,
+ 'h|?' => \$help,
+ 'help' => \$help,
+ 'man' => \$man,
+) or pod2usage(0);
+
+pod2usage(-verbose => 1) if $help;
+pod2usage(-verbose => 2) if $man;
+
+pod2usage(-msg => "$outPath doesn't exist please give a valid path", -verbose => 0) if (!-e $outPath);
+
+my @abbr = qw( Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec );
+
+open (my $MONF, ">$outPath/monthly.csv") or die "ERROR - unable to open \'$outPath/monthly.csv\': $!";
+open (my $DAYF, ">$outPath/daily.csv") or die "ERROR - unable to open \'$outPath/daily.csv\': $!";
+
+my %stats;
+my %dayStats;
+
+my $currMon = extract_stats(\%stats, \%dayStats, $file);
+
+my @monthly;
+my $i = 0;
+#print "Monthly summary.\n";
+## Sort by and then by month and output/store usage data for each month
+foreach my $yr (sort {$a <=> $b} keys %stats) {
+ #printf "\n%d\n", $yr + 1900;
+ foreach my $mon (sort {$a <=> $b} keys %{$stats{$yr}}) {
+ #print "$abbr[$mon]: $stats{$yr}{$mon}\n";
+ my $date = sprintf "%s %02d", $abbr[$mon], $yr-100;
+ print $MONF "$date,$stats{$yr}{$mon}\n";
+ $monthly[0][$i] = $date;
+ $monthly[1][$i] = $stats{$yr}{$mon};
+ ++$i;
+ }
+}
+draw_graph(\@monthly, 'Month', 'Monthly Breakdown of JNet Usage');
+
+my @daily;
+$i = 0;
+#print "\nDaily summary for $abbr[$currMon]\n";
+## Sort by date and ouput/store data for the current month.
+foreach my $day (sort {$a <=> $b} keys %dayStats) {
+ #printf "%02d: %d\n", $day, $dayStats{$day};
+ printf $DAYF "%02d,%d\n", $day, $dayStats{$day};
+ $daily[0][$i] = $day;
+ $daily[1][$i] = $dayStats{$day};
+ ++$i;
+}
+die "ERROR - No data for current month ($abbr[$currMon])" if (!@daily);
+draw_graph(\@daily, 'Date', "Daily Breakdown for $abbr[$currMon]");
+
+$i = 0;
+my @week;
+foreach my $num (-7..-1) {
+ next if (!$daily[0][$num]);
+ $week[0][$i] = sprintf "%02d/%02d", $daily[0][$num], $currMon+1;
+ $week[1][$i] = $daily[1][$num];
+ ++$i;
+}
+draw_sm_graph(\@week);
+exit;
+
+sub extract_stats {
+ my ($statsRef, $dayRef, $file) = @_;
+
+ open (my $FH, $file) or die "ERROR - can't open file \'$file\': $!";
+
+ my ($currMon, $currYr) = (localtime())[4,5];
+
+ while (<$FH>) {
+ next unless /www-jpred/;
+ my @F = split(/:/, $_);
+ die "ERROR - not enough fileds found in source file \'$file\'. Is the file correct and in the correct format?" if (9 > scalar @F);
+ #the 9th field is the date in Unix time. Extract the day, month and year from it.
+ my ($day, $mnth, $year) = (localtime($F[8]))[3..5];
+ next if ($year == 70); # ignore jobs with invalid dates
+ next if ($F[8] < 1148338800); # ignore jobs prior to 1 May 2006
+
+ if (($mnth == $currMon) && ($year == $currYr)) {
+ $dayRef->{$day}++;
+ }
+ $statsRef->{$year}{$mnth}++;
+ }
+ close($FH);
+ die "ERROR - no valid data found in \'$file\'" unless $statsRef; # die if there's no data in $statsRef
+ return ($currMon);
+}
+
+sub draw_graph {
+
+ my ($dataref, $x_label, $title) = @_;
+
+ my $graph = GD::Graph::bars->new(700, 400);
+
+ $graph->set_title_font("$FONTPATH/VeraBd.ttf", 12);
+ $graph->set_x_label_font("$FONTPATH/VeraBd.ttf", 8);
+ $graph->set_y_label_font("$FONTPATH/VeraBd.ttf", 8);
+ $graph->set_x_axis_font("$FONTPATH/Vera.ttf", 6);
+ $graph->set_y_axis_font("$FONTPATH/Vera.ttf", 8);
+ $graph->set(
+ x_label => $x_label,
+ y_label => 'No. JNet Submissions',
+ title => $title,
+ shadow_depth => -2,
+ shadowclr => 'gray',
+ x_labels_vertical => 1,
+ borderclrs => undef,
+ bar_width => 1,
+ bar_spacing => 4
+ ) or die $graph->error;
+
+ my $gd = $graph->plot($dataref) or die $graph->error;
+
+ open(IMG, ">$outPath/jnet_${x_label}_stats.png") or die $!;
+ binmode IMG;
+ print IMG $gd->png;
+ close(IMG);
+
+}
+
+sub draw_sm_graph {
+
+ my ($dataref) = @_;
+
+ my $graph = GD::Graph::bars->new(250, 150);
+
+ $graph->set_y_label_font("$FONTPATH/VeraBd.ttf", 8);
+ $graph->set_x_axis_font("$FONTPATH/Vera.ttf", 8);
+ $graph->set_y_axis_font("$FONTPATH/Vera.ttf", 8);
+ $graph->set(
+ y_label => 'No. Jobs',
+ x_labels_vertical => 1,
+ borderclrs => undef,
+ bar_width => 15,
+ accentclr => 'lbrown',
+ dclrs => [ qw(dbrown dpurple) ],
+ bar_spacing => 2
+ ) or die $graph->error;
+
+ my $gd = $graph->plot($dataref) or die $graph->error;
+
+ open(IMG, ">$outPath/jnet_stats.png") or die $!;
+ binmode IMG;
+ print IMG $gd->png;
+ close(IMG);
+
+}
+
+
+=head1 SYNOPSIS
+
+jpred_stats.pl [--path <path>] [--source <file>]
+
+=head1 DESCRIPTION
+
+Script to collate the usage statistics for the Jpred server. The stats are subdivided by month and then my day for he current month only.
+
+The outputs are two graph images <jnet_Month_stats.png> and <jnet_Date_stats.png> and two comma separated files (<monthly.csv> and <daily.csv>) containing the raw data.
+
+=head1 OPTIONS
+
+=over
+
+=item --path <path>
+
+Path to where you want the output saved. [default: <current directory>]
+
+=item --source <file>
+
+Source of Sun Grid Engine usage log file. [default: /grid/default/common/accounting]
+
+=item --help
+
+Display help.
+
+=item --man
+
+Display man page.
+
+=back
+
+By default the script with use the current known SGE logfile and output the data to current directory.
+
+=head1 AUTHOR
+
+Chris Cole <christian@cole.name>
+
+=cut
--- /dev/null
+#!/usr/bin/perl
+
+# hack to pull the alignments and profiles from psiblast
+
+# -m6 switch is needed to get the alignments
+# in the BLAST report, also generates the
+# psiblast frequency profiles, as they
+# are no longer present in the output
+
+use Getopt::Std;
+getopt(hfgud);
+
+if ($opt_f eq"req"){$freq=1}
+elsif ($opt_g eq "ap"){$gap=1}
+elsif ($opt_u eq "ngap"){$ungap=1}
+elsif ($opt_d eq "egap"){$degap=1}
+elsif ($opt_h eq "elp"){
+ print "
+# Parse_PSI
+
+This little script allows parsing of psiblast report files
+to extract the embedded sequence alignment, and write out
+in different formats.
+
+parse_psi -help : help
+parse_psi -degap : remove all gaps in alignment and print as
+ a fasta format file
+parse_psi -ungap : remove gaps in query sequence, and those
+ below the gap in the query sequence, print
+ as fasta format
+parse_psi -gap : print alignment with gaps in fasta format
+parse_psi -freq : print frequency profile needed for Jnet
+
+Usage:
+
+parse_psi -freq file.blast > file.freq
+\n";exit(0);
+}
+
+else {print "NO options given, try -help\n";exit}
+if (!-e "$ARGV[0]"){
+ print ("No such file as $ARGV[0] exists in this path...\n");
+ exit (0);
+}
+
+if ($ARGV[0] eq ""){
+ print "No filename given... \n";
+ exit;
+}
+
+open IN, "$ARGV[0]";
+$num=$thisone=$c=0;
+while(<IN>){
+ if (/^Sequences producing significant alignments/){
+ $num++;
+ }
+}
+print STDERR "$num alignments were found in PSIBlast file $ARGV[0]\n";
+$num--;
+
+close IN;
+open IN, "$ARGV[0]";
+while(<IN>){
+ if (/^Sequences producing significant alignments/){
+ if ($thisone == $num){
+ while (($ln2 = <IN>)){
+ if ($ln2 =~ /^QUERY/){
+ $alignout[$c]=$ln2;
+ $c++;
+ while (($align = <IN>) !~ /^ Database/){
+ $alignout[$c]=$align;
+ $c++;
+ }
+ last;
+ }
+ }
+ }
+ $thisone++;
+ }
+}
+
+$c=$j=$z=$blocks=0;
+
+# get number of blocks and number of sequences in a block
+
+foreach (@alignout){
+ if ($_ =~ /^\n/){
+ $blocks++;
+ }
+ if ($_ !~ /^\n/){
+ $store[$blocks][$z]=$_;
+ $z++;
+ }
+}
+$npb=($z/($blocks+1));
+
+for ($i=0; $i < ($blocks+1); $i++){
+ for ($j=0; $j < $npb ; $j++){
+ # get the alignment itself
+ #print "$store[$i][$q]";
+ (@tokens)=split(" ",$store[$i][$q]);
+ #print "$tokens[0] $tokens[1] $tokens[2] $tokens[3]\n";
+ if($#tokens == 3){
+ $id=$tokens[0];
+ $interest=$tokens[2];
+ }
+ if($#tokens == 1){
+ $id=$tokens[0];
+ $interest=$tokens[1];
+ }
+ if($#tokens == 2){
+ $id=$tokens[0];
+ $interest=$tokens[1];
+ if ($interest =~ /\d/g){
+ # get the next token, number
+ # must be at this end
+ $interest=$tokens[2];
+ }
+ }
+ # remove any digits that may creep in with the 3 token,
+ # this would mean the coord is on the end not in the
+ # middle.
+ $interest =~ s/\d//g;
+ undef @tokens;
+
+ $namekeep[$j]=$id;
+ $seqkeep[$j]=$seqkeep[$j].$interest;
+ $q++;
+ }
+}
+
+
+if ($gap==1 || $degap==1){
+ $c=0;
+ foreach (@seqkeep){
+
+ if ($degap==1){
+ $seqkeep[$c] =~ s/-//g;
+ }
+ print ">$namekeep[$c]\n$seqkeep[$c]\n";
+ $c++;
+ }
+}
+
+if ($ungap==1 || $freq == 1){
+ $c=0;
+
+ @sequence=split("",$seqkeep[0]);
+
+ foreach (@sequence){
+ if($sequence[$count] eq "\-"){
+ $printer[$count]=1;
+ }
+ else{$printer[$count]=0;}
+
+ $count++;
+ }
+ $d=0;
+ foreach $erm (@seqkeep){
+ undef @sequence;
+ @sequence=split("",$erm);
+ $count=0;
+ foreach (@sequence){
+ if ($printer[$count]==0){
+ $ung[$d]=$ung[$d].$sequence[$count];
+ }
+ $count++;
+ }
+ $d++;
+ }
+ if ($ungap == 1){
+ $c=0;
+ foreach $re (@ung){
+ print ">$namekeep[$c]\n$re\n";
+ $c++;
+ }
+ }
+ if ($freq == 1){
+ # do the counting....
+ $seqlen=length($ung[0]);
+
+ #get a double array
+ for ($i = 0; $i < $#ung; $i++){
+ undef @sequence;
+ @sequence=split("",$ung[$i]);
+
+ # convert sequence to an integer value
+ @ints = seq2int(@sequence);
+ $count=0;
+ $j=0;
+ foreach (@sequence) {
+ $ar[$i][$j]=$ints[$j];
+ $j++;
+ }
+ }
+
+ # zero countup
+ for ($r=0; $r <20; $r++){
+ $countup[$r]=0;
+ }
+
+ for ($i = 0; $i < $seqlen; $i++) {
+ # skip the query sequence
+ for ($j = 1; $j < $#ung ; $j++){
+ # look at array
+ $countup[$ar[$j][$i]]++;
+ }
+
+ # get total counts for this column
+ $tot = 0;
+ for ($r = 0; $r < 20; $r++){
+ $tot += $countup[$r];
+ }
+ for ($r=0; $r <20; $r++){
+ # get percent and round up to 10
+ # this seems to be slightly different to how
+ # psiblast works god knowns how....
+ # works for now. :-(
+ $outnum= ($countup[$r] / $tot ) * 10;
+ printf ("%2.0f ",$outnum);
+ $countup[$r]=0;
+ }
+ print "\n";
+ }
+ }
+}
+
+sub seq2int{
+ my(@s)=@_;
+ $g=0;
+ for ($g=0; $g <= $#s; $g++){
+ if ($s[$g] eq 'A'){ $intseq[$g] = "0"};
+ if ($s[$g] eq 'R'){ $intseq[$g] = "1"};
+ if ($s[$g] eq 'N'){ $intseq[$g] = "2"};
+ if ($s[$g] eq 'D'){ $intseq[$g] = "3"};
+ if ($s[$g] eq 'C'){ $intseq[$g] = "4"};
+ if ($s[$g] eq 'Q'){ $intseq[$g] = "5"};
+ if ($s[$g] eq 'E'){ $intseq[$g] = "6"};
+ if ($s[$g] eq 'G'){ $intseq[$g] = "7"};
+ if ($s[$g] eq 'H'){ $intseq[$g] = "8"};
+ if ($s[$g] eq 'I'){ $intseq[$g] = "9"};
+ if ($s[$g] eq 'L'){ $intseq[$g] = "10"};
+ if ($s[$g] eq 'K'){ $intseq[$g] = "11"};
+ if ($s[$g] eq 'M'){ $intseq[$g] = "12"};
+ if ($s[$g] eq 'F'){ $intseq[$g] = "13"};
+ if ($s[$g] eq 'P'){ $intseq[$g] = "14"};
+ if ($s[$g] eq 'S'){ $intseq[$g] = "15"};
+ if ($s[$g] eq 'T'){ $intseq[$g] = "16"};
+ if ($s[$g] eq 'W'){ $intseq[$g] = "17"};
+ if ($s[$g] eq 'Y'){ $intseq[$g] = "18"};
+ if ($s[$g] eq 'V'){ $intseq[$g] = "19"};
+ if ($s[$g] eq '-'){ $intseq[$g] = "25"};
+ }
+ return (@intseq);
+}
--- /dev/null
+#!/usr/bin/perl
+
+=head1 NAME
+
+prettify.pl
+
+=head1 SYNOPSYS
+
+prettify.pl [--blc I<path>] [--alscript I<path>] --postscript I<path>
+
+=head1 DESCRIPTION
+
+This program uses a BLC file to create an Alscript command file.
+
+=head1 TODO
+
+Add more options, make prettier Alscript command files.
+
+=head1 BUGS
+
+Alscript can't count properly and so we have to add one to some of the indicies to make it work.
+
+=head1 AUTHORS
+
+Started by Patrick Audley <paudley@compbio.dundee.ac.uk>
+Extended by Jonathan Barber <jon@compbio.dundee.ac.uk>
+
+=cut
+
+use strict;
+use warnings;
+use Getopt::Long;
+use BLC;
+
+my $prefix = "seq.protein";
+my $bin = "/software/submit_all";
+
+my $blc = '-';
+my $alscript = '-';
+my $psout;
+
+GetOptions(
+ "blc:s" => \$blc,
+ "alscript:s" => \$alscript,
+ "postscript=s" => \$psout,
+) or die "$!\n";
+
+die "--postscript option required\n" unless $psout;
+
+my $data = new BLC;
+$data->read_file($blc);
+
+# Find which entries for secondary structure are in the sequence data
+my @jpred = map { /^(?:jnet|jhmm|jalign|jpssm|lupas_14|lupas_21|lupas_28)$/ or 0 } $data->get_seq_ids;
+
+# Replace space characters with '-' for the FSM
+my @sequences = map { my $c = $_; $c =~ s/ /-/g; $c } $data->get_sequences;
+
+# Find the positions of the secondary structure in the BLC file
+my ($top, $bottom, $alignEnd);
+foreach (0 .. $#jpred) { $top = $_ and last if $jpred[$_] }
+foreach (reverse(0 .. $#jpred)) { $bottom = $_ and last if $jpred[$_] }
+my $end = length $sequences[0];
+
+# ... and then add 1 to them as Alscript can't count properly
+$alignEnd = $top;
+$top++;
+$bottom++;
+
+# alscript bits
+open ALSOUT, ">$alscript" or die "$alscript: Can't open the Alscript command file\n";
+
+# Commands for Alscript
+# Add one as Alscript can't count, and make sure it's over a minimum otherwise
+# it cores...
+my $foo = @sequences > 50 ? @sequences + 1 : 50;
+my $MAX_NSEQ = "MAX_NSEQ ".$foo;
+# Buffer size for reading the BLC file needs to be at least the size of alignment +2
+# This also needs to be larger than the longest line in the Alscript command file
+# If any lines are longer than MAX_INPUT_LEN then Alscript is likely to fail with 'success'
+my $MAX_INPUT_LEN = "MAX_INPUT_LEN ".($foo > 50 ? $foo + 2 : 50);
+my $BLOCK_FILE = '#';
+unless ($blc eq '-') { $BLOCK_FILE = "BLOCK_FILE $blc"; }
+my $OUTPUT_FILE = "OUTPUT_FILE $psout";
+
+# Print the header
+print ALSOUT <<END;
+SILENT_MODE
+$BLOCK_FILE
+$MAX_NSEQ
+$MAX_INPUT_LEN
+$OUTPUT_FILE
+PORTRAIT
+POINTSIZE 8
+IDENT_WIDTH 12
+X_OFFSET 2
+Y_OFFSET 2
+DEFINE_FONT 0 Helvetica DEFAULT
+DEFINE_FONT 1 Helvetica REL 0.75
+DEFINE_FONT 7 Helvetica REL 0.6
+DEFINE_FONT 3 Helvetica-Bold DEFAULT
+DEFINE_FONT 4 Times-Bold DEFAULT
+DEFINE_FONT 5 Helvetica-BoldOblique DEFAULT
+#
+DEFINE_COLOUR 3 1 0.62 0.67 # Turquiose
+DEFINE_COLOUR 4 1 1 0 # Yellow
+DEFINE_COLOUR 5 1 0 0 # Red
+DEFINE_COLOUR 7 1 0 1 # Purple
+DEFINE_COLOUR 8 0 0 1 # Blue
+DEFINE_COLOUR 9 0 1 0 # Green
+DEFINE_COLOUR 10 0.41 0.64 1.00 # Pale blue
+DEFINE_COLOUR 11 0.41 0.82 0.67 # Pale green
+DEFINE_COLOUR 50 0.69 0.18 0.37 # Pink (helix)
+DEFINE_COLOUR 51 1.00 0.89 0.00 # Gold (strand)
+NUMBER_INT 10
+SETUP
+#
+# Highlight specific residues.
+# Avoid highlighting Lupas 'C' predictions by
+# limiting the highlighting to the alignments
+Scol_CHARS C 1 1 $end $alignEnd 4
+Ccol_CHARS H ALL 5
+Ccol_CHARS P ALL 8
+SURROUND_CHARS LIV ALL
+#
+# Replace known structure types with whitespace
+SUB_CHARS 1 $top $end $bottom H SPACE
+SUB_CHARS 1 $top $end $bottom E SPACE
+SUB_CHARS 1 $top $end $bottom - SPACE
+END
+
+# Find the range of each of the secondary structure elements
+foreach (0..$#jpred) {
+ if ($jpred[$_]) { # Then it's a secondary structure definition
+ my $fsm = fsm($sequences[$_], qw(- E H c C));
+ my $line = $_ + 1;
+
+ foreach (@{$fsm->{'E'}}) {
+ my ($start, $end) = @{$_};
+ my $colour = 51;
+ print ALSOUT "STRAND $start $line $end\n";
+ print ALSOUT "COLOUR_TEXT_REGION $start $line $end $line $colour\n";
+ }
+
+ foreach (@{$fsm->{'H'}}) {
+ my ($start, $end) = @{$_};
+ my $colour = 50;
+ print ALSOUT "HELIX $start $line $end\n";
+ print ALSOUT "COLOUR_TEXT_REGION $start $line $end $line $colour\n";
+ }
+ }
+}
+
+# Munge out the jpred predictions using a basic FSM
+# Pass the sequence and the states that are present.
+# Returns HoA's, keys are the states, arrays are start and end
+# points of the states.
+# Idea taken from Patrick Audley
+sub fsm {
+ my ($sequence, @states) = @_;
+ my $state; # The state we're in
+ my $start = 0; # The start position of the current state
+ my %res; # Hash to store results in
+ my $pos = 0; # The position in the FSM
+
+ $state = substr $sequence, 0, 1;
+ foreach my $char (split //, $sequence) {
+ $pos++;
+ next if $char eq $state; # Same state
+
+ # Otherwise we've changed states
+ my $flag = 0;
+ foreach (@states) {
+ if ($_ eq $char) {
+ push @{$res{$state}}, [ $start, $pos - 1 ];
+ $state = $char;
+ $start = $pos;
+ $flag = 1;
+ last;
+ }
+ }
+ unless ($flag) {
+ warn "'$char' not a defined state at position $pos.\n";
+ }
+ }
+
+ return \%res;
+}
--- /dev/null
+#!/usr/bin/perl
+
+use strict;
+use warnings;
+
+if ($ARGV[0]) { open(IN, "<$ARGV[0]") or die($!); }
+else { *IN = *STDIN; }
+
+open(PROG, "| gs -dSAFER -q -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -sOutputFile=- -c .setpdfwrite -f -") or die($!);
+while (<IN>) { print PROG $_; }
+close(IN);
+close(PROG);
--- /dev/null
+#!/usr/bin/perl
+
+#
+# Program to query SWALL with a sequence and PSIBLAST and return the
+# profile, the PSIBLAST output and the alignment used by PSIBLAST.
+# The alignment is placed on STDOUT by default in FASTA format.
+#
+# --query <path> path to query in FASTA format
+# --profile <path> path to location for profile output
+# --blast <path> path to location for PSIBLAST output
+# --out <path> location for alignment output, defaults to STDOUT
+#
+
+use strict;
+use warnings;
+use Getopt::Long;
+
+use lib '/homes/www-jpred/new_site/bin64';
+
+use jpred;
+
+# Modified function which uses fastacmd rather the indexing
+# scheme used the db_dbindex db creation script. This is useful
+# as the previous method was 32- bit dependent.
+# - CC 30/08/06
+sub getseq {
+ my ($hash_ref) = shift @_;
+
+ foreach my $seqID (keys %{$hash_ref}) {
+
+ next if ($seqID eq 'QUERY'); # skip query sequence
+
+ my $seq;
+
+ open(FCMD, "$BINDIR/fastacmd -d $SWALL -s $seqID |") or die "unable to retrieve sequence $seqID from database $SWALL: $!";
+ while (<FCMD>) {
+ chomp;
+ next if /^>/; # skip desc line
+ $seq .= $_; #
+ }
+ close(FCMD);
+ if (!$seq) {
+ die "ERROR - $seqID has no sequence in SWALL database.\n";
+ }
+ ${$hash_ref}{$seqID} = $seq;
+ }
+}
+
+my ($out, $query, $profile, $blast) = qw(-);
+GetOptions(
+ "query=s" => \$query,
+ "profile=s" => \$profile,
+ "blast=s" => \$blast,
+ "out:s" => \$out
+);
+
+die "no query sequence path given\n" unless $query;
+die "no profile output path given\n" unless $profile;
+die "no BLAST output path given\n" unless $blast;
+
+xsystem("$BINDIR/blastpgp -e0.05 -h0.01 -m6 -b20000 -j3 -d $SWALLFILT -i $query -Q $profile -o $blast");
+
+# Find the number of passes and get the position at which the sequences
+# start, plus find the length of the query to check if it has been shortened
+# in the alignment later on.
+my $position;
+my $queryLength = 0;
+open BLAST, "<$blast" or die "$blast: $!\n";
+while (<BLAST>) {
+
+ if (/\((\d+) letters\)/) {
+ $queryLength = $1;
+ }
+
+ if (/^Sequences used in model and found/) {
+ <BLAST>;
+ $position = tell BLAST;
+ }
+}
+
+# Check we found some sequences (FIXME: may need to be more robust)
+unless ($position) {
+ warn "PSIBLAST found no homologous sequences and couldn't construct an alignment. As Jpred requires a multiple alignment it couldn't continue.\n";
+ die "Jpred failed\n";
+}
+
+if (!$queryLength) {
+ warn "unable to match query length\n";
+}
+
+# Get the sequences used and their alignments
+seek BLAST, $position, 0;
+my (@alignments, @order, $flag, %seqid);
+while (<BLAST>) {
+ # Get the alignments
+ if (/^QUERY/) {
+ my $id = (split ' ', $_)[0];
+ push @order, $id;
+ $seqid{$id} = undef;
+
+ chomp;
+ push @alignments, $_;
+
+ while (<BLAST>) {
+ last if /^ Database: /;
+ last if /^ \*{5} No hits found \*{5}/;
+ last if /^Searching/;
+ # Only bother getting the sequence ID's
+ # from the first block of alignments...
+ if (/^\n/) { $flag = 1, next }
+ unless ($flag) { # Get the sequence ID
+ my $id = (split " ", $_)[0];
+ push @order, $id;
+ $seqid{$id} = undef;
+ }
+ # ...but continue adding the sequences from the alignments
+ chomp;
+ push @alignments, $_;
+ }
+ }
+}
+close BLAST;
+
+# Get the ID and sequence for each of the alignment sequence
+&getseq(\%seqid);
+
+# Replace the X's in the alignment with their proper characters
+# Add these onto @sequences
+my @sequences;
+my $padStart;
+my $padEnd;
+foreach (0..$#alignments) {
+ my $i = $_ % @order;
+ my ($seqid, $start, $seq, $end) = split ' ', $alignments[$_], 4;
+
+ # blastpgp output allways has a ID at the begining of the line,
+ # but can have a variable number of fields after that, but it
+ # means the sequence contains no characters of interest
+ # e.g.:
+# $seqid $start $seq $end
+# O24727 ------------------------------------------------------------
+# O24727 0 ------------------------------------------------------------
+# O24727 26 -Y--A---A-----L-----R----S-------L---------G-------P----V--- 35
+ unless ($end) {
+ unless ($seq) {
+ $sequences[$i] .= $start;
+ next;
+ }
+ else {
+ $sequences[$i] .= $seq;
+ next;
+ }
+ }
+
+ # Don't do anything for the query sequence, but check whether the ends have been chopped off
+ if ($i == 0) {
+ if ( ($_ == 0) && ($start != 1) ) {
+ #warn "QUERY doesn't start at the beginning! ($start)\n";
+ $padStart = '-'x($start-1);
+ }
+ if ((scalar @alignments/scalar @order == ($_/scalar @order) +1 ) && ($queryLength != $end)) {
+ my $diff = $queryLength - $end;
+ #warn "end is missing from QUERY! ($diff)\n";
+ $padEnd = '-'x$diff;
+ }
+ $sequences[$i] .= $seq;
+ next;
+ }
+
+ my @seq = split '', $seq;
+ my $j = 0;
+ foreach (@seq) {
+ # Skip gaps and blanks, don't add one to the counter ($j)
+ # expect for proper characters.
+ next if $_ eq '-' or $_ eq ' ';# /[ -]/;
+
+ if (/X/) {
+ unless ($seqid{$seqid}) {
+ die "Internal conflict between SWISS-PROT and BLAST databases (were they built from the same data?): $seqid has was not found.\n";
+ }
+ # If the length of the sequence is less than
+ # where we're accessing it from there's a problem.
+ if (length $seqid{$seqid} < $start + $j) {
+ warn length $seqid{$seqid}, ", $start, $j, $seqid, $seqid{$seqid}, $i\n";
+ }
+
+ # - 1 as start is indexed from 1...
+ $_ = substr($seqid{$seqid}, $start + $j - 1, 1);
+ }
+ $j++;
+ }
+ $sequences[$i] .= join '', @seq;
+}
+
+## If BLAST has shortened the query sequence replace the missing residues
+## in the QUERY and pad the other sequences with gaps
+if ($padEnd or $padStart) {
+ warn "BLAST has shortened the query sequence. Getting original query and padding aligned matches.\n";
+
+ ## get query sequence
+ my $querySeq;
+ open(my $FH, $query) or die "$query: $!";
+ while(<$FH>) {
+ next if (/>/);
+ chomp;
+ $querySeq .= $_;
+ }
+ close($FH);
+ die "Unable to find a sequence in file: $query" if (!$querySeq);
+
+ ## correct sequences
+ if ($padEnd) {
+ my $len = length($padEnd);
+ my $pad = substr($querySeq, -$len); # grab right no. of residues from end of query
+ $sequences[0] .= $pad; # add missing residues to end of query
+ $sequences[$_] .= $padEnd for (1..$#order); # add equivalent no. of gaps in hit seqs
+ }
+ if ($padStart) {
+ my $len = length($padStart);
+ my $pad = substr($querySeq, 0, $len); # grab right no. of residues from start of query
+ $sequences[0] = $pad.$sequences[0]; # add missing residues to start of query
+ $sequences[$_] = $padStart.$sequences[$_] for (1..$#order); # add equivalent no. of gaps in hit seqs
+ }
+}
+
+# Print the results in FASTA, replace QUERY with filename of query,
+# prints them in order in the profile occurance, if two (or more) local
+# alignments occur in one sequence, print them as seperate results
+open OUT, ">$out" or die "$out: $!\n";
+foreach (0..$#order) {
+ print OUT ">$order[$_]\n";
+ $sequences[$_] =~ s/(.{72})/$1\n/g;
+ print OUT $sequences[$_], "\n";
+}
+close OUT;
+
+# Remove zero sized error logs that blastpgp helpfully creates
+if (-e 'error.log' && ! -z 'error.log') {
+ warn "blastpgp wrote error log file\n";
+}
+else {
+ unlink "error.log";
+}
--- /dev/null
+#!/usr/bin/perl
+
+# script to run a specified jpred pipeline on a given
+# sequence. Helps to separate the running of Jpred/Jnet
+# from any pre-/post-processing of data.
+
+=head1 NAME
+
+run_jpred.pl - a wrapper to run Jpred
+
+=cut
+
+use warnings;
+use strict;
+use Getopt::Long;
+use Pod::Usage;
+
+use lib "/homes/www-jpred/new_site/bin64";
+
+use jpred;
+
+use lib '/homes/chris/lib';
+
+use Jpred::jnetDB;
+
+my $pipe = 'jpred3'; # specify which Jpred pipeline to use (not sure which ones work anymore)
+my $jnet = '2.2'; # specify which version of Jnet to use (input paramters changed following 2.1)
+my $useLocal; # do prediction on cluster node's local disk
+my $useDB = 0; # find query sequences in DB for array jobs
+my $path; # output path for results
+my $fasta; # input sequence in Fasta format
+my $help;
+my $man;
+
+GetOptions(
+ 'seq=s' => \$fasta,
+ 'pipe=s' => \$pipe,
+ 'out=s' => \$path,
+ 'use-local' => \$useLocal,
+ 'jnet=s' => \$jnet,
+ 'use-db!' => \$useDB,
+ 'help|?' => \$help,
+ 'man' => \$man
+) or pod2usage(0);
+
+pod2usage(-verbose => 2) if $man;
+pod2usage(-verbose => 1) if $help;
+
+## check to see if in array context
+my $seqID = $ENV{'SGE_TASK_ID'};
+undef $seqID if ($seqID eq 'undefined');
+
+pod2usage(-msg => 'Please give a sequence filename or run as an array job on the cluster', -verbose => 0) if (!$fasta && !$seqID);
+pod2usage(-msg => 'Please give an output path', -verbose => 0) if !$path;
+
+chdir($path) or die "ERROR - unable to cd to \'$path\': $!\nDied";
+
+my $clustDir;
+my $msf = 0;
+if ($seqID) {
+ ## we're cluster array context
+ printf "On cluster node: %s\n", `hostname`;
+
+ if ($useLocal) {
+ ## find temporary directory on local disk
+ $clustDir = $ENV{TMPDIR};
+ print "Cluster TMPDIR: $clustDir\n";
+ }
+
+ if ($useDB) {
+ ##retrieve data from DB
+ print "Retrieving $seqID from JnetDB...\n";
+ my $dbh = connect_DB('ro');
+ my $seq = get_seq($dbh, $seqID);
+ die "ERROR - '$seqID' not found in DB.\nDied" unless ($seq);
+ $dbh->disconnect();
+ if ($clustDir) {
+ $fasta = "$clustDir/$seqID.fasta";
+ } else {
+ $fasta = "$path/$seqID.fasta";
+ }
+
+ ## write seq data to file
+ open(my $fh, ">$fasta") or die "ERROR - '$fasta': $!";
+ print $fh ">$seqID\n$seq\n";
+ close($fh);
+ } else {
+ ## else get it from the file
+ $fasta = "$seqID.fasta";
+ die "ERROR - file '$fasta' doesn't exits.\nDied" unless (-e $fasta);
+
+ if ($clustDir) {
+ system("cp $fasta $clustDir/$seqID.fasta") == 0 or die "ERROR - unable to copy '$fasta' to '$clustDir/$seqID.fasta'\nDied";
+ } else {
+ system("cp $fasta $path/$seqID.fasta") == 0 or die "ERROR - unable to copy '$fasta' to '$path/$seqID.fasta'\nDied";
+ }
+
+ }
+} elsif ($fasta) {
+ if ($fasta =~ /\/*([^\/]+)?\.fas/) {
+ $seqID = $1;
+ } elsif ($fasta =~ /\/*([^\/]+)?\.msf/) {
+ print "Found an alignement file...\n";
+ $seqID = $1;
+ $msf = 1;
+ } else {
+ die "ERROR - unable to match for \'$fasta\'";
+ }
+
+} else {
+ die "ERROR - unknown error ;)";
+}
+
+if (-e "$seqID.jnet") {
+ print "Prediction already exists for '$seqID'. Stopping...\n";
+ my @del = glob "*.e*.$seqID";
+ unlink(@del);
+ exit;
+}
+
+if ($pipe eq 'new') {
+ #
+ # cp seq input file to out dir if not already there
+ #
+ mkdir($seqID) or die "ERROR - can't mkdir \'$seqID\': $!\nDied";
+ chdir($seqID) or die "ERROR - can't chdir \'$seqID\': $!\nDied";
+ if (!-e "$seqID.fasta") {
+ system("cp $path/$fasta $seqID.fasta") == 0 or die "ERROR - \'cp $path/$fasta $path/$seqID/$seqID.fasta\' failed to run";
+ }
+
+ my $cmd = "$JPREDROOT/new_pipeline/jpred --seq $seqID.fasta --output $seqID --db swall";
+ system($cmd) == 0 or error("$JPREDROOT/new_pipeline/jpred", $seqID);
+ unless ($?) { # when Jnet successfully finishes, copy output files to directory where 'validate_jnet' can find them.
+ chdir('..');
+ system("ln -s $seqID/$seqID.jnet $seqID.jnet");
+ system("ln -s $seqID/$seqID.align $seqID.align");
+ my @clust = glob "$path/*.$seqID";
+ unlink(@clust);
+ }
+ exit;
+}
+
+
+if ($msf) {
+ #
+ # if input is an alignment reformat it and generate an HMM profile
+ #
+ reformat($fasta, $seqID);
+ my $error = get_hmm($seqID);
+ if ($error) {
+ error($error, $seqID);
+ exit(1);
+ }
+
+
+} else {
+ #
+ # cp seq input file to out dir if not already there
+ #
+ if (!-e "$seqID.fasta") {
+ system("cp $fasta $seqID.fasta") == 0 or die "ERROR - \'cp $fasta $path/$seqID.fasta\' failed to run";
+ }
+
+ #
+ # check we know which pipeline to use and run it
+ #
+ if ($pipe eq 'cuff') {
+ my $error = old_pipeline($seqID);
+ if ($error) {
+ error($error, $seqID);
+ exit(1);
+ }
+ } elsif ($pipe eq 'jpred2') {
+ my $error = jpred2_pipe($seqID);
+ if ($error) {
+ error($error, $seqID);
+ exit(1);
+ }
+ } elsif ($pipe eq 'jpred3') {
+ my $dir;
+ if ($useLocal) {
+ $dir = $clustDir;
+ } else {
+ $dir = $path;
+ }
+ my $error = jpred3_pipe($seqID, $dir);
+ if ($error) {
+ error($error, $seqID);
+ exit(1);
+ }
+ if ($useLocal) {
+ print "Rsyncing...\n";
+ system("rsync -az $clustDir/$seqID.* $path/") == 0 or die "ERROR - system() rsync command fails: $?\nDied";
+ }
+ exit;
+ } else {
+ die "ERROR - unknown pipeline \'$pipe\'\n";
+ }
+}
+
+#
+# run Jnet
+#
+my $cmd;
+# QSUB IGNORE $cmd = "$BINDIR/jnet_tng --cross 1 --hmm_prof $seqID.hmmprof --psi_prof $seqID.pssm --freq $seqID.freq > $seqID.jnet";
+if ($msf) {
+ #
+ # only JNet 2.2 can be run with a pre-generated alignment
+ #
+ $cmd = "$BINDIR/jnet --concise --sequence $seqID.align --hmmer $seqID.hmmprof > $seqID.jnet";
+} else {
+ #
+ # generate correct command sytax dependent on version of JNet
+ #
+ if ($jnet > 2.1) {
+ $cmd = "$BINDIR/jnet --concise --sequence $seqID.align --hmmer $seqID.hmmprof --psiprof $seqID.pssm --psifreq $seqID.freq > $seqID.jnet";
+ } elsif ($jnet eq '2') {
+ $cmd = "$BINDIR/jnet.orig -c $seqID.align $seqID.hmmprof $seqID.pssm $seqID.freq > $seqID.jnet";
+ } else {
+ die "ERROR - unknown version of JNet \'$jnet\'\n";
+ }
+}
+print "Running: $cmd\n";
+system($cmd) == 0 or error("$BINDIR/jnet", $seqID);
+exit(1) if $?;
+
+exit(0);
+
+sub jpred3_pipe {
+ my ($seqID, $localDir) = @_;
+
+ my $run_cmd = "/homes/www-jpred/new_site/jpred_new/jpred --seq $localDir/$seqID.fasta --output $localDir/$seqID --db uniref90 --verbose";
+ print "--CMD $run_cmd\n";
+ system($run_cmd) == 0 or return('jpred3');
+ return(0);
+}
+
+sub old_pipeline {
+
+ # original JNet pipeline used for the James Cuff version
+ # of the software. Runs all of the necessary scripts to generate
+ # input for JNet.
+
+ # NB to compare with the 2000 paper requires at least 2 hits to
+ # the query for PSI-BLAST runs. NOT USED AT THE MOMENT
+
+ my ($seqID, $seq) = @_;
+
+ my $cmd = "$BINDIR/blastpgp -d $SWALLFILT -b20000 -a2 -j3 -e0.05 -h0.01 -m6 -i $seqID.fasta -Q $seqID.pssm -o $seqID.blast";
+ print "Running: $cmd\n";
+ system($cmd) == 0 or return("$BINDIR/blastpgp");
+
+ print "Runing: $BINDIR/parse_psi -freq $seqID.blast > $seqID.freq\n";
+ system("$BINDIR/parse_psi -freq $seqID.blast > $seqID.freq") == 0
+ or return("$BINDIR/parse_psi -freq");
+
+ print "Runing: $BINDIR/parse_psi -ungap $seqID.blast > $seqID.align\n";
+ system("$BINDIR/parse_psi -ungap $seqID.blast > $seqID.align") == 0
+ or return("$BINDIR/parse_psi -ungap");
+ #my $num = `grep -c '>' $seqID.align`;
+ #return("Insufficient PSI-BLAST hits") if ($num < 3); # need at least 2 hits to query (2+1 = 3) to get a decent profile
+
+ print "Running: $BINDIR/fasta2msf < $seqID.align > $seqID.msf\n";
+ system("$BINDIR/fasta2msf < $seqID.align > $seqID.msf") == 0
+ or return("$BINDIR/fasta2msf");
+
+ print "Running: $BINDIR/hmmbuild -F --fast --gapmax 1 --wblosum ${seqID}_tmp.hmm $seqID.msf";
+ system("$BINDIR/hmmbuild -F --fast --gapmax 1 --wblosum ${seqID}_tmp.hmm $seqID.msf") == 0
+ or return("$BINDIR/hmmbuild");
+
+ print "Running: $BINDIR/hmmconvert -F -p ${seqID}_tmp.hmm ${seqID}_tmp.prof\n";
+ system("$BINDIR/hmmconvert -F -p ${seqID}_tmp.hmm ${seqID}_tmp.prof") == 0
+ or return("$BINDIR/hmmconver");
+
+ print "Running: $BINDIR/hmm2profile ${seqID}_tmp.prof > $seqID.hmmprof\n";
+ system("$BINDIR/hmm2profile ${seqID}_tmp.prof > $seqID.hmmprof") == 0
+ or return("$BINDIR/hmm2profile");
+ unlink("${seqID}_tmp.prof", "${seqID}_tmp.hmm");
+
+ return(0);
+}
+
+sub jpred2_pipe {
+
+ # current pipeline as used by the Jpred server.
+
+ # NB to compare with the 2000 paper requires at least 2 hits to
+ # the query for PSI-BLAST runs. NOT USED AT THE MOMENT
+
+ my ($seqID, $seq) = @_;
+
+ my $cmd = "$BINDIR/psiblast --query $seqID.fasta --profile $seqID.profile --blast $seqID.blast > $seqID.alignment";
+ print "Running: $cmd\n";
+ system($cmd) == 0 or return("$BINDIR/psiblast");
+ #my $num = `grep -c '>' $seqID.alignment`;
+ #return("Insufficient PSI-BLAST hits") if ($num < 3); # need at least 2 hits to query (2+1 = 3) to get a decent profile
+
+ $cmd = "$BINDIR/reduce --limit 1000 < $seqID.alignment > $seqID.align";
+ print "Running: $cmd\n";
+ system($cmd) == 0 or return("$BINDIR/reduce");
+
+ $cmd = "$BINDIR/nonred --cutoff 75 --in $seqID.align --out $seqID.oc > $seqID.align.fasta";
+ print "Running: $cmd\n";
+ system($cmd) == 0 or return("$BINDIR/nonred");
+
+ $cmd = "$BINDIR/trim_seqs --factor 1.5 < $seqID.align.fasta > ${seqID}_tmp";
+ print "Running: $cmd\n";
+ system($cmd) == 0 or return("$BINDIR/trim_seqs");
+ if (fasta_chk_no_seqs("${seqID}_tmp") < 2) {
+ warn "Warning - Trimmed too many sequences from alignment. Now using all BLAST hits.\n";
+ system("cp $seqID.alignment $seqID.align.fasta") == 0 or return("\'cp $seqID.alignment $seqID.align.fasta\'");
+ } else {
+ rename("${seqID}_tmp", "$seqID.align.fasta");
+ }
+
+ #$cmd = "$JAVABIN -jar $BINDIR/readseq.jar -fMSF -a -p < $seqID.align.fasta > $seqID.align.msf";
+ #print "Running: $cmd\n";
+ #system($cmd) == 0 or return("$BINDIR/readseq");
+
+ $cmd = "$BINDIR/clean_fasta $seqID.align.fasta > ${seqID}_tmp";
+ print "Running: $cmd\n";
+ system($cmd) == 0 or return("$BINDIR/clean_fasta");
+ rename("${seqID}_tmp", "$seqID.align.fasta");
+
+ $cmd = "$BINDIR/fasta2upper < $seqID.align.fasta > ${seqID}_tmp";
+ print "Running: $cmd\n";
+ system($cmd) == 0 or return("$BINDIR/fasta2upper");
+ rename("${seqID}_tmp", "$seqID.align.fasta");
+
+ $cmd = "$BINDIR/fasta2jnet < $seqID.align.fasta > $seqID.align";
+ print "Running: $cmd\n";
+ system($cmd) == 0 or return("$BINDIR/fasta2jnet");
+
+ #$cmd = "$JAVABIN -jar $BINDIR/readseq.jar -fMSF -a -p < $seqID.align > $seqID.align.msf";
+ #print "Running: $cmd\n";
+ #system($cmd) == 0 or return("$BINDIR/readseq");
+
+ $cmd = "$BINDIR/profile < $seqID.align > $seqID.freq";
+ print "Running: $cmd\n";
+ system($cmd) == 0 or return("$BINDIR/profile");
+
+ $cmd = "$BINDIR/getpssm < $seqID.profile > $seqID.pssm";
+ print "Running: $cmd\n";
+ system($cmd) == 0 or return("$BINDIR/getpssm");
+
+ ## use fasta input rather than msf as sometimes fails. Is it due to faults in readseq above?
+ #$cmd = "$BINDIR/gethmm -in $seqID.align.msf -out $seqID.hmmprof > /dev/null";
+ $cmd = "$BINDIR/gethmm -in $seqID.align -out $seqID.hmmprof > /dev/null";
+ print "Running: $cmd\n";
+ system($cmd) == 0 or return("$BINDIR/gethmm");
+
+ return(0);
+}
+
+sub error {
+
+ my ($app, $seq) = @_;
+
+ warn "ERROR - $app failed to run for $seq\n";
+}
+
+sub reformat {
+
+ my ($file, $seqID) = @_;
+
+ system("$BINDIR/readseq -fMSF -a -p < $file > $seqID.align.msf");
+ if ($?) {
+ error("$BINDIR/readseq", $seqID);
+ exit;
+ }
+ system("$BINDIR/readseq -f8 -a -p < $seqID.align.msf > $seqID.align.fas")
+
+}
+
+sub get_hmm {
+ my ($seqID) = @_;
+
+ $cmd = "$BINDIR/gethmm -in $seqID.align.msf -out $seqID.hmmprof > /dev/null";
+ print "Running: $cmd\n";
+ system($cmd) == 0 or return("$BINDIR/gethmm");
+
+ return(0);
+
+}
+sub fasta_chk_no_seqs { # taken from 'webrun' in the Jpred suite of scripts
+ my $file = shift;
+ open my $fh, $file or die "$!: $file";
+ my $i = 0;
+ local $/ = "\n";
+ while (<$fh>) { $i++ if /^>/ }
+ close $fh;
+ return $i;
+}
+
+=head1 SYNOPSIS
+
+run_jpred.pl --seq <sequence filename> --out <path> --pipe <name> --jnet <version> [--use-local] [--use-db] [--help] [--man]
+
+=head1 DESCRIPTION
+
+Jpred is made up of a whole host of scripts and programs which prepare the inputs/outputs to/from the JNet code. Doing this manually is pretty painful and not recommended :-)
+
+This wrapper should make life a lot easier whereby the user simply supplies a sequence (or a multiple alignment) and the script does the rest.
+
+Due to all the programs that this wrapper encompasses there are many output files generated (at least one for each step), but the main Jpred prediction is found in the .jnet file. All the other files may be of use, but that's up to you to decide...
+
+Now the script can be run as an array job while connecting to the jnetDB. This should make running large Jpred runs on the cluster much more efficient.
+
+=head1 OPTIONS
+
+=over 8
+
+=item B<--seq> <sequence filename>
+
+Optional: if a filename is not supplied then cluster array context is assumed.
+
+This can either be a fasta-formatted file with a single sequence or a multiple sequence alignment in B<msf> format. The file should have the extension .fas* or .msf
+
+=item B<--out> <path>
+
+Required.
+
+Path to where the results files are to be stored.
+
+=item B<--pipe> <name>
+
+Select which pipeline is required. There are currently three options: 'cuff', 'jpred2' and 'jpred3'. As the names suggest the 'cuff' pipeline is the one used (as far as I can tell) by James Cuff and the 'server' is the one used by the, erm, server.
+
+Default: 'jpred3'
+
+=item B<--jnet> <version>
+
+Select which version of JNet is required to generate the secondary structure prediction. There are currently two options: '2' and '2.2'. JNet v2 is the original version as created by James Cuff and v2.2 is the bug-fixed version updated by Jon Barber as used by the server.
+
+Default: 2.2
+
+=item B<--use-local>
+
+For cluster use only. Use the local disk as a working directory. [Default: off]
+
+=item B<--use-db>
+
+In array context retrieve the files from the Jnet database, otherwise assume they're on disk. [Default: off]
+
+=back
+
+I B<strongly> recommend that users only run using the default settings for --pipe and --jnet as things are liable to break otherwise. Those options are mainly for me to do benchmarking between different versions and are specific to my setup. I don't think this is a problem as the defaults simply use what the Jpred server uses, which will be what you want 99.9% of the time. The other 0.01% is your problem ;-)
+
+=head1 EXAMPLES
+
+To simply run on a machine:
+
+ run_jpred.pl --seq test.fas --out my_results/
+
+will run PSI-BLAST and everything else on test.fas and the JNet output will be found in my_results/test.jnet
+
+To submit to the cluster nodes:
+
+ qsub -q 64bit.q -cwd -S /usr/bin/perl run_jpred.pl --seqtest.fas --out my_results/
+
+and the results will be found in the same place.
+
+To submit an array job for sequences 100-200 from jnetDB:
+
+ qsub -t 100-200 -q 64bit.q -cwd -S /usr/bin/perl run_jpred.pl --out my_results/
+
+=head1 BUGS
+
+There are currenly no known bugs...
+
+=head1 VERSION
+
+This is version 0.5
+
+=head1 AUTHOR
+
+Chris Cole <christian@cole.name>
+
+=cut
--- /dev/null
+#!/usr/bin/perl
+
+=head1 NAME
+
+run_large_data.pl - script to run a large dataset against Jpred using the cluster
+
+=cut
+
+use strict;
+use warnings;
+
+use Getopt::Long;
+use Pod::Usage;
+use File::Basename;
+
+# temporary. Should put this module somewhere more global.
+use lib '/homes/ccole/lib';
+use Cluster::ArrayJob 0.3;
+
+my $file;
+my $scriptName = "jpredLarge.pl";
+my $title = 'jpredLarge';
+my $VERBOSE = 0;
+my $DEBUG = 0;
+my $help;
+my $man;
+
+GetOptions (
+ 'in=s' => \$file,
+ 'title=s' => \$title,
+ 'verbose!' => \$VERBOSE,
+ 'debug!' => \$DEBUG,
+ 'man' => \$man,
+ 'help|?' => \$help,
+) or pod2usage();
+
+pod2usage(-verbose => 2) if ($man);
+pod2usage(-verbose => 1) if ($help);
+pod2usage(-msg => 'Please supply a valid filename.') if (!$file or !-e $file);
+
+print "Reading fasta file...\n";
+my $total = split_fasta($file);
+print "Created $total fasta files\n";
+
+write_script($scriptName);
+
+
+## set up Array Job and submit perl script
+## Just use all the defaults.
+print "Submitting $total Jpred jobs to the cluster as an array job...\n" if $VERBOSE;
+my $sgeArray = Cluster::ArrayJob->new();
+$sgeArray->taskRange("1-$total");
+$sgeArray->queue('64bit-pri.q');
+$sgeArray->setCWD();
+$sgeArray->jobname($title);
+$sgeArray->setJobShare(0);
+$sgeArray->setPriority(-100);
+$sgeArray->setResourceRequest( 'ram' => '6G' );
+$sgeArray->setEnv( 'PERL5LIB' => '/homes/www-jpred/live/lib' );
+$sgeArray->submit($scriptName);
+
+print "Checking status of array job...\n" if $VERBOSE;
+while (1) {
+ my $status = $sgeArray->getStatus() or die "ERROR - unable to get SGE job status: ", $sgeArray->error();
+ if ($status eq '-1') {
+ print "Job has finished\n" if $VERBOSE;
+ last;
+ } elsif ($status eq '1') {
+ die "ERROR - unable to get SGE job status: ", $sgeArray->error();
+ } else {
+ my $out = '';
+ foreach my $k (sort keys %$status) {
+ $out .= " $k:".$status->{$k};
+ }
+ print "Job status: $out\n" if $VERBOSE;
+ }
+ sleep(30);
+}
+
+## Finally, check that all jobs completed successfully.
+my $jobID = $sgeArray->jobid();
+my @files = glob "$title.e$jobID.*";
+
+my $errors = 0;
+## check that the correct number of SGE files exist - should be the same as the number of tasks
+my $nFiles = scalar @files;
+if ($nFiles != $total) {
+ warn "Warning - found $nFiles SGE output files where $total expected\n";
+ ++$errors;
+}
+
+## check that the right number of Jnet outputs were generated
+my @jnets = glob "*.jnet";
+my $nJnets = scalar @jnets;
+if ($total != $nJnets) {
+ warn "Warning - found $nJnets Jnet predictions where $total expected\n";
+}
+print "All Jpred searches completed!\n";
+exit;
+
+
+## write script with code from __DATA__ below
+sub write_script {
+ my $file = shift;
+
+ open(my $OUT, ">$file") or die "ERROR - unable to open file '$file': $!\n";
+ while (<DATA>) {
+ print $OUT $_;
+ }
+ close($OUT);
+ close(DATA);
+}
+
+## short function to split a Fasta file
+## into one file per sequence
+sub split_fasta {
+ my $file = shift;
+
+ open(my $FAS, "<", $file) or die "ERROR - unable to open '$file': ${!}\nDied";
+ my $num = 0;
+ my $OUT;
+ while(<$FAS>) {
+ ## check first line has appriate start
+ if ($. == 1) {
+ die "ERROR - this file does not appear to be a Fasta file\n" unless (/^>/);
+ }
+ ## for each new record open a new file and close the preceeding one
+ if (/^>/) {
+ ++$num;
+ my $out = "$num.fasta";
+ close($OUT) if ($OUT); # needed for first one; can't close if nothing's open
+ open($OUT, ">", $out) or die "ERROR - unable to open '$out' for write: ${!}\nDied";
+ }
+ print $OUT $_;
+
+ }
+ close($OUT);
+ return($num)
+}
+
+=head1 SYNOPSIS
+
+run_large_data.pl --in <file> [--verbose] [--debug] [--man] [--help]
+
+=head1 DESCRIPTION
+
+Running a large set of sequences against Jpred can be a but of a pain as Jpred can be very memory intensive and can take a while.
+
+Therefore, use of the cluster is best, but managing the jobs can be a bit fiddly. So, this script does it all for you!
+
+Just provide a Fasta file with all the sequences you want to run and the script will submit each of them to the cluster separately, monitor their progress and report if there have been any failures. Job done!
+
+=head1 OPTIONS
+
+=over 5
+
+=item B<--in>
+
+Input file (fasta format).
+
+=item B<--verbose|--no-verbose>
+
+Toggle verbosity. [default:none]
+
+=item B<--debug|--no-debug>
+
+Toggle debugging output. [default:none]
+
+=item B<--help>
+
+Brief help.
+
+=item B<--man>
+
+Full manpage of program.
+
+=back
+
+=head1 AUTHOR
+
+Chris Cole <christian@cole.name>
+
+=cut
+
+__DATA__
+#!/usr/bin/perl
+
+use strict;
+use warnings;
+
+my $pwd = $ENV{PWD}; # get current directory
+my $dir = $ENV{TMPDIR}; # get SGE tmpdir
+my $task = $ENV{'SGE_TASK_ID'}; # get SGE array task ID
+die "ERROR - not in SGE array job context. Please submit as an array job.\n" if (!$task or $task eq 'undefined');
+
+die "ERROR - file '$task.fasta' not found at '$pwd'. Check path.\n" unless (-e "$task.fasta");
+if (-s "$task.jnet") {
+ print "A Jnet prediction already exists for '$task.fasta'. Skipping...\n";
+ exit();
+}
+
+my $cmd = "cd $dir && /homes/www-jpred/live/jpred/jpred --sequence $pwd/$task.fasta --output $task";
+print "Running CMD: $cmd\n";
+system($cmd) == 0 or die "ERROR - system() died\n";
+if (-s "$dir/$task.jnet") {
+ print "Jnet successful! Copying files from cluster to $pwd...";
+ system("cp $dir/$task.* $pwd/") ==0 or die "ERROR - system() died\n";
+ print "Done\n";
+} else {
+ #my $out = `ls -ltr $dir`;
+ #print "ls -ltr:\n$out\n";
+ print "No Jnet prediction found for '$task'. Something failed...\n"
+}
--- /dev/null
+#!/usr/bin/perl
+#
+
+#
+# Wrapper for multicoil and ncoil to generate csv style output to STDOUT
+# Pass it the complete path to the sequence or multicoil will complain
+#
+# multicoils ignored as it's a bitch to setup
+
+use strict;
+use warnings;
+use POSIX;
+use Jpred;
+
+unless (@ARGV) { die("No arguments given\n"); }
+goto NCOILS;
+my ($path) = $ENV{'PWD'};
+my ($file) = ($ARGV[0] =~ /.*\/(.*)/);
+my ($multicoil) = ($ENV{'PAIRCOIL_CONFIG'} =~ /(.*)\/.*/);
+
+# Print multicoils cmd file to temp file
+my $multi_conf = tmpnam();
+open(FILE, ">$multi_conf") or die($!);
+print FILE "method = MultiCoil
+bound = .5
+no GUI
+window length = 28
+multi_lib 1 = 3 4 5
+multi_lib 2 = 2 3 4
+pair_lib = 1 2 4
+conversion dir = $multicoil/CONVERSION_FILES/
+table 1 = $multicoil/PROGRAM_DATA/cctb28
+table 2 = $multicoil/PROGRAM_DATA/tritb28
+pir = $multicoil/PROGRAM_DATA/sampled-pir.seq
+genbnk = $multicoil/PROGRAM_DATA/genbnk
+printfile dir = /homes/jon/jpred/src/MULTICOIL/TEST_RUNS/
+log dir = $path/
+seq scores dir = $path/
+out dir = $path/";
+close(FILE);
+
+my $tmp2 = tmpnam();
+xsystem("$BINDIR/readseq -f3 -p < $ARGV[0] > $tmp2");
+
+# 1, 2, 3! We hate multicoil! Have to be in the same path as it's exe
+# to run due to the hex editing on the multicoil exe to allow it to read
+# some of its data files, also it requires PIR input file, sigh...
+#my $pwd = $ENV{'PWD'};
+#chdir("$JPREDROOT/src/MULTICOIL/");
+#xsystem("$JPREDROOT/src/MULTICOIL/multicoil $tmp2 -config $multi_conf > /dev/null 2> /dev/null");
+#chdir($pwd);
+
+#my $co=0;
+#my (@prob, @dimprob, @trimprob);
+
+#$tmp2 =~ s/.*\///g;
+
+#open(IN, "<$path/$tmp2.out") or die($!);
+#while (<IN>) {
+# if (/^[#|%]/) { next; }
+# else {
+# @_ = split(" ", $_);
+# push @prob, $_[4];
+# push @dimprob, $_[5];
+# push @trimprob, $_[6];
+# }
+# }
+#close(IN);
+
+# remove junk
+#unlink("$tmp2.out");
+#unlink("$tmp2.seq_scores");
+#unlink("$tmp2.log");
+#unlink $multi_conf, $tmp2;
+
+# Takes the prob. array and decides whether it's definitely a coil,
+# maybe a coil, or not a coil.
+sub coil {
+ my @array;
+ foreach (@_) {
+ if ($_ >= 0.9) {
+ push @array, "C";
+ }
+ elsif ($_ >= 0.5) {
+ push @array, "c";
+ }
+ else {
+ push @array, "-";
+ }
+ }
+ return @array;
+ }
+
+# Prints a comma after each piece of data in array
+
+sub print_cvs {
+ foreach (@_) { print "$_,"; }
+}
+
+#print "MULTCOIL:";
+#print_cvs(coil(@prob));
+#print "\n", "MULTCOIL_DIMER:";
+#print_cvs(coil(@dimprob));
+#print "\n", "MULTCOIL_TRIMER:";
+#print_cvs(coil(@trimprob));
+#print "\n";
+
+#
+# Finished with multicoil, now for lupas coils (?) Just runs ncoils with
+# different -win values
+#
+
+sub ncoils {
+ my ($file, $window) = @_;
+ my @temp;
+ open(PROG, "$BINDIR/ncoils -w -win $window < $file |") or die($!);
+ open(REALDATA, ">$ARGV[0].lupas_$window") or die($!);
+ while (<PROG>) {
+ print REALDATA "$_";
+ chop;
+ push @temp, substr($_, 19, 5);
+ }
+ close(PROG);
+ close(REALDATA);
+ return @temp;
+ }
+
+NCOILS:
+print "Lupas_21:";
+print_cvs(coil(ncoils($ARGV[0], 21))); # 21 window
+print "\n", "Lupas_14:";
+print_cvs(coil(ncoils($ARGV[0], 14))); # 14 window
+print "\n", "Lupas_28:";
+print_cvs(coil(ncoils($ARGV[0], 28))); # 28 window
+print "\n";
+
--- /dev/null
+# Matrix made by matblas from blosum45.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 45
+# Entropy = 0.3795, Expected = -0.2789
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 5 -2 -1 -2 -1 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -2 -2 0 -1 -1 -1 -5
+R -2 7 0 -1 -3 1 0 -2 0 -3 -2 3 -1 -2 -2 -1 -1 -2 -1 -2 -1 0 -1 -5
+N -1 0 6 2 -2 0 0 0 1 -2 -3 0 -2 -2 -2 1 0 -4 -2 -3 4 0 -1 -5
+D -2 -1 2 7 -3 0 2 -1 0 -4 -3 0 -3 -4 -1 0 -1 -4 -2 -3 5 1 -1 -5
+C -1 -3 -2 -3 12 -3 -3 -3 -3 -3 -2 -3 -2 -2 -4 -1 -1 -5 -3 -1 -2 -3 -1 -5
+Q -1 1 0 0 -3 6 2 -2 1 -2 -2 1 0 -4 -1 0 -1 -2 -1 -3 0 4 -1 -5
+E -1 0 0 2 -3 2 6 -2 0 -3 -2 1 -2 -3 0 0 -1 -3 -2 -3 1 4 -1 -5
+G 0 -2 0 -1 -3 -2 -2 7 -2 -4 -3 -2 -2 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -5
+H -2 0 1 0 -3 1 0 -2 10 -3 -2 -1 0 -2 -2 -1 -2 -3 2 -3 0 0 -1 -5
+I -1 -3 -2 -4 -3 -2 -3 -4 -3 5 2 -3 2 0 -2 -2 -1 -2 0 3 -3 -3 -1 -5
+L -1 -2 -3 -3 -2 -2 -2 -3 -2 2 5 -3 2 1 -3 -3 -1 -2 0 1 -3 -2 -1 -5
+K -1 3 0 0 -3 1 1 -2 -1 -3 -3 5 -1 -3 -1 -1 -1 -2 -1 -2 0 1 -1 -5
+M -1 -1 -2 -3 -2 0 -2 -2 0 2 2 -1 6 0 -2 -2 -1 -2 0 1 -2 -1 -1 -5
+F -2 -2 -2 -4 -2 -4 -3 -3 -2 0 1 -3 0 8 -3 -2 -1 1 3 0 -3 -3 -1 -5
+P -1 -2 -2 -1 -4 -1 0 -2 -2 -2 -3 -1 -2 -3 9 -1 -1 -3 -3 -3 -2 -1 -1 -5
+S 1 -1 1 0 -1 0 0 0 -1 -2 -3 -1 -2 -2 -1 4 2 -4 -2 -1 0 0 -1 -5
+T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -1 -1 2 5 -3 -1 0 0 -1 -1 -5
+W -2 -2 -4 -4 -5 -2 -3 -2 -3 -2 -2 -2 -2 1 -3 -4 -3 15 3 -3 -4 -2 -1 -5
+Y -2 -1 -2 -2 -3 -1 -2 -3 2 0 0 -1 0 3 -3 -2 -1 3 8 -1 -2 -2 -1 -5
+V 0 -2 -3 -3 -1 -3 -3 -3 -3 3 1 -2 1 0 -3 -1 0 -3 -1 5 -3 -3 -1 -5
+B -1 -1 4 5 -2 0 1 -1 0 -3 -3 0 -2 -3 -2 0 0 -4 -2 -3 4 2 -1 -5
+Z -1 0 0 1 -3 4 4 -2 0 -3 -2 1 -1 -3 -1 0 -1 -2 -2 -3 2 4 -1 -5
+X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -5
+* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1
--- /dev/null
+# Matrix made by matblas from blosum62.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 62
+# Entropy = 0.6979, Expected = -0.5209
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 -1 -4
+R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -4
+N -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -4
+D -2 -2 1 6 -3 0 2 -1 -1 -3 -4 -1 -3 -3 -1 0 -1 -4 -3 -3 4 1 -1 -4
+C 0 -3 -3 -3 9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -1 -4
+Q -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 3 -1 -4
+E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4
+G 0 -2 0 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -4
+H -2 0 1 -1 -3 0 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 0 -1 -4
+I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -3 -1 3 -3 -3 -1 -4
+L -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -4 -3 -1 -4
+K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 -1 -3 -1 0 -1 -3 -2 -2 0 1 -1 -4
+M -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 0 -2 -1 -1 -1 -1 1 -3 -1 -1 -4
+F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -1 -4
+P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2 -2 -1 -1 -4
+S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 0 -1 -4
+T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -2 -2 0 -1 -1 -1 -4
+W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11 2 -3 -4 -3 -1 -4
+Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -2 -1 -4
+V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -4
+B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 1 -1 -4
+Z -1 0 0 1 -3 3 4 -2 0 -3 -3 1 -1 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4
+X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -4
+* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 1
--- /dev/null
+# Matrix made by matblas from blosum80.iij
+# * column uses minimum score
+# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
+# Blocks Database = /data/blocks_5.0/blocks.dat
+# Cluster Percentage: >= 80
+# Entropy = 0.9868, Expected = -0.7442
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 5 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 1 0 -3 -2 0 -2 -1 -1 -6
+R -2 6 -1 -2 -4 1 -1 -3 0 -3 -3 2 -2 -4 -2 -1 -1 -4 -3 -3 -2 0 -1 -6
+N -2 -1 6 1 -3 0 -1 -1 0 -4 -4 0 -3 -4 -3 0 0 -4 -3 -4 4 0 -1 -6
+D -2 -2 1 6 -4 -1 1 -2 -2 -4 -5 -1 -4 -4 -2 -1 -1 -6 -4 -4 4 1 -1 -6
+C -1 -4 -3 -4 9 -4 -5 -4 -4 -2 -2 -4 -2 -3 -4 -2 -1 -3 -3 -1 -4 -4 -1 -6
+Q -1 1 0 -1 -4 6 2 -2 1 -3 -3 1 0 -4 -2 0 -1 -3 -2 -3 0 3 -1 -6
+E -1 -1 -1 1 -5 2 6 -3 0 -4 -4 1 -2 -4 -2 0 -1 -4 -3 -3 1 4 -1 -6
+G 0 -3 -1 -2 -4 -2 -3 6 -3 -5 -4 -2 -4 -4 -3 -1 -2 -4 -4 -4 -1 -3 -1 -6
+H -2 0 0 -2 -4 1 0 -3 8 -4 -3 -1 -2 -2 -3 -1 -2 -3 2 -4 -1 0 -1 -6
+I -2 -3 -4 -4 -2 -3 -4 -5 -4 5 1 -3 1 -1 -4 -3 -1 -3 -2 3 -4 -4 -1 -6
+L -2 -3 -4 -5 -2 -3 -4 -4 -3 1 4 -3 2 0 -3 -3 -2 -2 -2 1 -4 -3 -1 -6
+K -1 2 0 -1 -4 1 1 -2 -1 -3 -3 5 -2 -4 -1 -1 -1 -4 -3 -3 -1 1 -1 -6
+M -1 -2 -3 -4 -2 0 -2 -4 -2 1 2 -2 6 0 -3 -2 -1 -2 -2 1 -3 -2 -1 -6
+F -3 -4 -4 -4 -3 -4 -4 -4 -2 -1 0 -4 0 6 -4 -3 -2 0 3 -1 -4 -4 -1 -6
+P -1 -2 -3 -2 -4 -2 -2 -3 -3 -4 -3 -1 -3 -4 8 -1 -2 -5 -4 -3 -2 -2 -1 -6
+S 1 -1 0 -1 -2 0 0 -1 -1 -3 -3 -1 -2 -3 -1 5 1 -4 -2 -2 0 0 -1 -6
+T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -2 -1 -1 -2 -2 1 5 -4 -2 0 -1 -1 -1 -6
+W -3 -4 -4 -6 -3 -3 -4 -4 -3 -3 -2 -4 -2 0 -5 -4 -4 11 2 -3 -5 -4 -1 -6
+Y -2 -3 -3 -4 -3 -2 -3 -4 2 -2 -2 -3 -2 3 -4 -2 -2 2 7 -2 -3 -3 -1 -6
+V 0 -3 -4 -4 -1 -3 -3 -4 -4 3 1 -3 1 -1 -3 -2 0 -3 -2 4 -4 -3 -1 -6
+B -2 -2 4 4 -4 0 1 -1 -1 -4 -4 -1 -3 -4 -2 0 -1 -5 -3 -4 4 0 -1 -6
+Z -1 0 0 1 -4 3 4 -3 0 -4 -3 1 -2 -4 -2 0 -1 -4 -3 -3 0 4 -1 -6
+X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -6
+* -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 1
--- /dev/null
+; comments must have a semicolon in the first column or else
+; unpredictable behavior after reading the file will result
+; the first value is the type of filter; the second is info; then data
+1 1 = filter 2 = matrix
+250 if 1, window if 2, cutoff
+100 { symbol "A", name "Adenine" },
+33 { symbol "B" , name "G or T or C" },
+0 { symbol "C", name "Cytosine" },
+67 { symbol "D", name "G or A or T" },
+; { symbol "", name "" },
+; { symbol "", name "" },
+0 { symbol "G", name "Guanine" },
+67 { symbol "H", name "A or C or T" } ,
+; { symbol "", name "" },
+; { symbol "", name "" },
+50 { symbol "K", name "G or T" },
+; { symbol "", name ""},
+50 { symbol "M", name "A or C" },
+50 { symbol "N", name "A or G or C or T" } ,
+; { symbol "", name "" },
+; { symbol "", name "" },
+; { symbol "", name ""},
+50 { symbol "R", name "G or A"},
+0 { symbol "S", name "G or C"},
+100 { symbol "T", name "Thymine"},
+; { symbol "", name ""},
+33 { symbol "V", name "G or C or A"},
+0 { symbol "W", name "A or T" },
+; { symbol "", name ""},
+50 { symbol "Y", name "T or C"}
--- /dev/null
+;Chothia aa ; 16 character descriptor
+;2 ; 1=Nucleic 2=Protein
+1 ; 1=Filter 2-64=No. Pos. in Matrix
+8 ; 3-256=Filter Window 0-100=Percent Cutoff Matrix Output
+ -0.27 A Ala
+ 0.55 BB Asx
+ -0.23 C Cys Note: Columns 1-8 must contain 1 numeric value only
+ 0.50 D Asp
+ 0.33 E Glu
+ -0.55 F Phe
+ -0.22 G Gly
+ 0.37 H His
+ -0.80 I Ile
+ 1.17 K Lys
+ -0.44 L Leu
+ -0.31 M Met
+ 0.61 N Asn
+ 0.36 P Pro
+ 1.00 Q Gln
+ 2.00 R Arg
+ 0.17 S Ser
+ 0.18 T Thr
+ -0.65 V Val
+ 0.05 W Trp
+ 0.19 X- Unk
+ 0.48 Y Tyr
+ 0.66 ZZ Glx
+ 0.19 ** ***
+;Chothia -- dunno -- picked out of a FORTRAN file from Spouge
--- /dev/null
+; comments must have a semicolon in the first column or else
+; unpredictable behavior after reading the file will result
+; the first value is the type of filter; the second is info; then data
+1 1 = filter 2 = matrix
+250 if 1, window if 2, cutoff
+0 { symbol "A", name "Adenine" },
+67 { symbol "B" , name "G or T or C" },
+100 { symbol "C", name "Cytosine" },
+33 { symbol "D", name "G or A or T" },
+; { symbol "", name "" },
+; { symbol "", name "" },
+100 { symbol "G", name "Guanine" },
+33 { symbol "H", name "A or C or T" } ,
+; { symbol "", name "" },
+; { symbol "", name "" },
+50 { symbol "K", name "G or T" },
+; { symbol "", name ""},
+50 { symbol "M", name "A or C" },
+50 { symbol "N", name "A or G or C or T" } ,
+; { symbol "", name "" },
+; { symbol "", name "" },
+; { symbol "", name ""},
+50 { symbol "R", name "G or A"},
+100 { symbol "S", name "G or C"},
+0 { symbol "T", name "Thymine"},
+; { symbol "", name ""},
+67 { symbol "V", name "G or C or A"},
+0 { symbol "W", name "A or T" },
+; { symbol "", name ""},
+50 { symbol "Y", name "T or C"}
--- /dev/null
+;Antigenicity ; 16 character descriptor
+;2 ; 1=Nucleic 2=Protein
+1 ; 1=Filter 2-64=No. Pos. in Matrix
+6 ; 3-256=Filter Window 0-100=Percent Cutoff Matrix Output
+ -0.500 A Ala
+ 1.600 BB Asx
+ -1.000 C Cys Note: Columns 1-8 must contain 1 numeric value only
+ 3.000 D Asp
+ 3.000 E Glu
+ -2.500 F Phe
+ 0.000 G Gly
+ -0.500 H His
+ -1.800 I Ile
+ 3.000 K Lys
+ -1.800 L Leu
+ -1.300 M Met
+ 0.200 N Asn
+ 0.000 P Pro
+ 0.200 Q Gln
+ 3.000 R Arg
+ 0.300 S Ser
+ -0.400 T Thr
+ -1.500 V Val
+ -3.400 W Trp
+ -0.200 X- Unk
+ -2.300 Y Tyr
+ 1.600 ZZ Glx
+ -0.200 ** ***
+;Antigenicity - Hopp and Woods (Hydrophilicity Index)
+;A window of 6 residues is the published (and recomended)
+;value for calculating the moving average
--- /dev/null
+;Hydropathy ; 16 character descriptor
+;2 ; 1=Nucleic 2=Protein
+1 ; 1=Filter 2-64=No. Pos. in Matrix
+19 ; 3-256=Filter Window 0-100=Percent Cutoff Matrix Output
+ 1.800 A Ala
+ -3.500 BB Asx
+ 2.500 C Cys Note: Columns 1-8 must contain 1 numeric value only
+ -3.500 D Asp
+ -3.500 E Glu Note: This file is required for amphpathic helic
+ 2.800 F Phe
+ -0.400 G Gly
+ -3.200 H His
+ 4.500 I Ile
+ -3.900 K Lys
+ 3.800 L Leu
+ 1.900 M Met
+ -3.500 N Asn
+ -1.600 P Pro
+ -3.500 Q Gln
+ -4.500 R Arg
+ -0.800 S Ser
+ -0.700 T Thr
+ 4.200 V Val
+ -0.900 W Trp
+ -0.490 X- Unk
+ -1.300 Y Tyr
+ -3.500 ZZ Glx
+ -0.490 ** ***
+;Hydropathy - Kyte and Doolittle (Hydrophobicity Index)
+;A window of 19 residues is the published (and recomended) value
+;for calculating the moving average to find membrane spanning regions
--- /dev/null
+; original matrix
+A 1.297 1.551 1.084 2.612 0.377 1.248 0.877 ; A
+B 0.000 0.000 0.000 0.000 0.000 0.000 0.000 ; BDN
+C 0.824 0.022 0.308 0.152 0.180 0.156 0.044 ; C
+D 0.030 2.352 2.268 0.237 0.663 1.620 1.448 ; D
+E 0.262 3.496 3.108 0.998 5.685 2.494 3.048 ; E
+F 0.531 0.076 0.403 0.662 0.189 0.106 0.013 ; F
+G 0.045 0.275 0.578 0.216 0.211 0.426 0.156 ; G
+H 0.347 0.275 0.679 0.395 0.294 0.579 0.213 ; H
+I 2.597 0.098 0.345 0.894 0.514 0.471 0.431 ; I
+K 1.375 2.639 1.763 0.191 1.815 1.961 2.795 ; K
+L 3.167 0.297 0.398 3.902 0.585 0.501 0.483 ; L
+M 2.240 0.370 0.480 1.409 0.541 0.772 0.663 ; M
+N 0.835 1.475 1.534 0.039 1.722 2.456 2.280 ; N
+P 0.000 0.008 0.000 0.013 0.000 0.000 0.000 ; P
+Q 0.179 2.114 1.778 0.631 2.550 1.578 2.526 ; Q
+R 0.659 1.163 1.210 0.031 1.358 1.937 1.798 ; R
+S 0.382 0.583 1.052 0.419 0.525 0.916 0.628 ; S
+T 0.169 0.702 0.955 0.654 0.791 0.843 0.647 ; T
+V 1.665 0.403 0.386 0.949 0.211 0.342 0.360 ; V
+W 0.240 0.000 0.000 0.456 0.019 0.000 0.000 ; W
+X 0.000 0.000 0.000 0.000 0.000 0.000 0.000 ; X-
+Y 1.417 0.090 0.122 1.659 0.190 0.130 0.155 ; Y
+Z 0.000 0.000 0.000 0.000 0.000 0.000 0.000 ; ZEQ
+* 0.000 0.000 0.000 0.000 0.000 0.000 0.000 ; **
--- /dev/null
+; comments must have a semicolon in the first column or else
+; unpredictable behavior after reading the file will result
+; the first value is the type of filter; the second is info; then data
+1 1 = filter 2 = matrix
+250 if 1, window if 2, cutoff
+100 { symbol "A", name "Adenine" },
+33 { symbol "B" , name "G or T or C" },
+0 { symbol "C", name "Cytosine" },
+67 { symbol "D", name "G or A or T" },
+; { symbol "", name "" },
+; { symbol "", name "" },
+100 { symbol "G", name "Guanine" },
+33 { symbol "H", name "A or C or T" } ,
+; { symbol "", name "" },
+; { symbol "", name "" },
+50 { symbol "K", name "G or T" },
+; { symbol "", name ""},
+50 { symbol "M", name "A or C" },
+50 { symbol "N", name "A or G or C or T" } ,
+; { symbol "", name "" },
+; { symbol "", name "" },
+; { symbol "", name ""},
+100 { symbol "R", name "G or A"},
+50 { symbol "S", name "G or C"},
+0 { symbol "T", name "Thymine"},
+; { symbol "", name ""},
+67 { symbol "V", name "G or C or A"},
+50 { symbol "W", name "A or T" },
+; { symbol "", name ""},
+0 { symbol "Y", name "T or C"}
--- /dev/null
+; comments must have a semicolon in the first column or else
+; unpredictable behavior after reading the file will result
+; the first value is the type of filter; the second is info; then data
+1 1 = filter 2 = matrix
+250 if 1, window if 2, cutoff
+0 { symbol "A", name "Adenine" },
+67 { symbol "B" , name "G or T or C" },
+100 { symbol "C", name "Cytosine" },
+33 { symbol "D", name "G or A or T" },
+; { symbol "", name "" },
+; { symbol "", name "" },
+0 { symbol "G", name "Guanine" },
+67 { symbol "H", name "A or C or T" } ,
+; { symbol "", name "" },
+; { symbol "", name "" },
+50 { symbol "K", name "G or T" },
+; { symbol "", name ""},
+50 { symbol "M", name "A or C" },
+50 { symbol "N", name "A or G or C or T" } ,
+; { symbol "", name "" },
+; { symbol "", name "" },
+; { symbol "", name ""},
+0 { symbol "R", name "G or A"},
+50 { symbol "S", name "G or C"},
+100 { symbol "T", name "Thymine"},
+; { symbol "", name ""},
+33 { symbol "V", name "G or C or A"},
+0 { symbol "W", name "A or T" },
+; { symbol "", name ""},
+100 { symbol "Y", name "T or C"}
--- /dev/null
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 30 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -5.06, Entropy = 2.57 bits
+#
+# Lowest score = -17, Highest score = 13
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 6 -7 -4 -3 -6 -4 -2 -2 -7 -5 -6 -7 -5 -8 -2 0 -1 -13 -8 -2 -3 -3 -3 -17
+R -7 8 -6 -10 -8 -2 -9 -9 -2 -5 -8 0 -4 -9 -4 -3 -6 -2 -10 -8 -7 -4 -6 -17
+N -4 -6 8 2 -11 -3 -2 -3 0 -5 -7 -1 -9 -9 -6 0 -2 -8 -4 -8 6 -3 -3 -17
+D -3 -10 2 8 -14 -2 2 -3 -4 -7 -12 -4 -11 -15 -8 -4 -5 -15 -11 -8 6 1 -5 -17
+C -6 -8 -11 -14 10 -14 -14 -9 -7 -6 -15 -14 -13 -13 -8 -3 -8 -15 -4 -6 -12 -14 -9 -17
+Q -4 -2 -3 -2 -14 8 1 -7 1 -8 -5 -3 -4 -13 -3 -5 -5 -13 -12 -7 -3 6 -5 -17
+E -2 -9 -2 2 -14 1 8 -4 -5 -5 -9 -4 -7 -14 -5 -4 -6 -17 -8 -6 1 6 -5 -17
+G -2 -9 -3 -3 -9 -7 -4 6 -9 -11 -10 -7 -8 -9 -6 -2 -6 -15 -14 -5 -3 -5 -5 -17
+H -7 -2 0 -4 -7 1 -5 -9 9 -9 -6 -6 -10 -6 -4 -6 -7 -7 -3 -6 -1 -1 -5 -17
+I -5 -5 -5 -7 -6 -8 -5 -11 -9 8 -1 -6 -1 -2 -8 -7 -2 -14 -6 2 -6 -6 -5 -17
+L -6 -8 -7 -12 -15 -5 -9 -10 -6 -1 7 -8 1 -3 -7 -8 -7 -6 -7 -2 -9 -7 -6 -17
+K -7 0 -1 -4 -14 -3 -4 -7 -6 -6 -8 7 -2 -14 -6 -4 -3 -12 -9 -9 -2 -4 -5 -17
+M -5 -4 -9 -11 -13 -4 -7 -8 -10 -1 1 -2 11 -4 -8 -5 -4 -13 -11 -1 -10 -5 -5 -17
+F -8 -9 -9 -15 -13 -13 -14 -9 -6 -2 -3 -14 -4 9 -10 -6 -9 -4 2 -8 -10 -13 -8 -17
+P -2 -4 -6 -8 -8 -3 -5 -6 -4 -8 -7 -6 -8 -10 8 -2 -4 -14 -13 -6 -7 -4 -5 -17
+S 0 -3 0 -4 -3 -5 -4 -2 -6 -7 -8 -4 -5 -6 -2 6 0 -5 -7 -6 -1 -5 -3 -17
+T -1 -6 -2 -5 -8 -5 -6 -6 -7 -2 -7 -3 -4 -9 -4 0 7 -13 -6 -3 -3 -6 -4 -17
+W -13 -2 -8 -15 -15 -13 -17 -15 -7 -14 -6 -12 -13 -4 -14 -5 -13 13 -5 -15 -10 -14 -11 -17
+Y -8 -10 -4 -11 -4 -12 -8 -14 -3 -6 -7 -9 -11 2 -13 -7 -6 -5 10 -7 -6 -9 -7 -17
+V -2 -8 -8 -8 -6 -7 -6 -5 -6 2 -2 -9 -1 -8 -6 -6 -3 -15 -7 7 -8 -6 -5 -17
+B -3 -7 6 6 -12 -3 1 -3 -1 -6 -9 -2 -10 -10 -7 -1 -3 -10 -6 -8 6 0 -5 -17
+Z -3 -4 -3 1 -14 6 6 -5 -1 -6 -7 -4 -5 -13 -4 -5 -6 -14 -9 -6 0 6 -5 -17
+X -3 -6 -3 -5 -9 -5 -5 -5 -5 -5 -6 -5 -5 -8 -5 -3 -4 -11 -7 -5 -5 -5 -5 -17
+* -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 1
--- /dev/null
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 70 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -2.77, Entropy = 1.60 bits
+#
+# Lowest score = -11, Highest score = 13
+#
+ A R N D C Q E G H I L K M F P S T W Y V B Z X *
+A 5 -4 -2 -1 -4 -2 -1 0 -4 -2 -4 -4 -3 -6 0 1 1 -9 -5 -1 -1 -1 -2 -11
+R -4 8 -3 -6 -5 0 -5 -6 0 -3 -6 2 -2 -7 -2 -1 -4 0 -7 -5 -4 -2 -3 -11
+N -2 -3 6 3 -7 -1 0 -1 1 -3 -5 0 -5 -6 -3 1 0 -6 -3 -5 5 -1 -2 -11
+D -1 -6 3 6 -9 0 3 -1 -1 -5 -8 -2 -7 -10 -4 -1 -2 -10 -7 -5 5 2 -3 -11
+C -4 -5 -7 -9 9 -9 -9 -6 -5 -4 -10 -9 -9 -8 -5 -1 -5 -11 -2 -4 -8 -9 -6 -11
+Q -2 0 -1 0 -9 7 2 -4 2 -5 -3 -1 -2 -9 -1 -3 -3 -8 -8 -4 -1 5 -2 -11
+E -1 -5 0 3 -9 2 6 -2 -2 -4 -6 -2 -4 -9 -3 -2 -3 -11 -6 -4 2 5 -3 -11
+G 0 -6 -1 -1 -6 -4 -2 6 -6 -6 -7 -5 -6 -7 -3 0 -3 -10 -9 -3 -1 -3 -3 -11
+H -4 0 1 -1 -5 2 -2 -6 8 -6 -4 -3 -6 -4 -2 -3 -4 -5 -1 -4 0 1 -3 -11
+I -2 -3 -3 -5 -4 -5 -4 -6 -6 7 1 -4 1 0 -5 -4 -1 -9 -4 3 -4 -4 -3 -11
+L -4 -6 -5 -8 -10 -3 -6 -7 -4 1 6 -5 2 -1 -5 -6 -4 -4 -4 0 -6 -4 -4 -11
+K -4 2 0 -2 -9 -1 -2 -5 -3 -4 -5 6 0 -9 -4 -2 -1 -7 -7 -6 -1 -2 -3 -11
+M -3 -2 -5 -7 -9 -2 -4 -6 -6 1 2 0 10 -2 -5 -3 -2 -8 -7 0 -6 -3 -3 -11
+F -6 -7 -6 -10 -8 -9 -9 -7 -4 0 -1 -9 -2 8 -7 -4 -6 -2 4 -5 -7 -9 -5 -11
+P 0 -2 -3 -4 -5 -1 -3 -3 -2 -5 -5 -4 -5 -7 7 0 -2 -9 -9 -3 -4 -2 -3 -11
+S 1 -1 1 -1 -1 -3 -2 0 -3 -4 -6 -2 -3 -4 0 5 2 -3 -5 -3 0 -2 -1 -11
+T 1 -4 0 -2 -5 -3 -3 -3 -4 -1 -4 -1 -2 -6 -2 2 6 -8 -4 -1 -1 -3 -2 -11
+W -9 0 -6 -10 -11 -8 -11 -10 -5 -9 -4 -7 -8 -2 -9 -3 -8 13 -3 -10 -7 -10 -7 -11
+Y -5 -7 -3 -7 -2 -8 -6 -9 -1 -4 -4 -7 -7 4 -9 -5 -4 -3 9 -5 -4 -7 -5 -11
+V -1 -5 -5 -5 -4 -4 -4 -3 -4 3 0 -6 0 -5 -3 -3 -1 -10 -5 6 -5 -4 -2 -11
+B -1 -4 5 5 -8 -1 2 -1 0 -4 -6 -1 -6 -7 -4 0 -1 -7 -4 -5 5 1 -2 -11
+Z -1 -2 -1 2 -9 5 5 -3 1 -4 -4 -2 -3 -9 -2 -2 -3 -10 -7 -4 1 5 -3 -11
+X -2 -3 -2 -3 -6 -2 -3 -3 -3 -3 -4 -3 -3 -5 -3 -1 -2 -7 -5 -2 -2 -3 -3 -11
+* -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 1
--- /dev/null
+PrintTemplateSet ::= {
+ {
+ name "StdSeqDescrElement" ,
+ format {
+ asn1 "Seq-descr.E" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Seq-descr.E.mol-type" ,
+ label "Molecule type" ,
+ prefix " " ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "Seq-descr.E.modif" ,
+ label "Modifiers" ,
+ prefix " " ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Seq-descr.E.modif.E" ,
+ form
+ enum {
+ } } } } } ,
+ {
+ asn1 "Seq-descr.E.method" ,
+ label "Method" ,
+ prefix " " ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "Seq-descr.E.name" ,
+ label "Name" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Seq-descr.E.title" ,
+ label "Title" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Seq-descr.E.org" ,
+ label "Organism" ,
+ prefix " " ,
+ form
+ use-template "StdOrgRef" } ,
+ {
+ asn1 "Seq-descr.E.comment" ,
+ label "Comment" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Seq-descr.E.num" ,
+ label "Numbering" ,
+ prefix " " ,
+ form
+ use-template "StdNumbering" } ,
+ {
+ asn1 "Seq-descr.E.maploc" ,
+ label "Map location" ,
+ prefix " " ,
+ form
+ use-template "StdDbtag" } ,
+ {
+ asn1 "Seq-descr.E.pir" ,
+ label "PIR block" ,
+ prefix " " ,
+ form
+ null NULL } ,
+ {
+ asn1 "Seq-descr.E.genbank" ,
+ label "GenBank block" ,
+ prefix " " ,
+ form
+ null NULL } ,
+ {
+ asn1 "Seq-descr.E.pub" ,
+ label "Citation" ,
+ prefix " " ,
+ form
+ use-template "StdPubdesc" } ,
+ {
+ asn1 "Seq-descr.E.region" ,
+ label "Region" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Seq-descr.E.user" ,
+ label "User Type" ,
+ prefix " " ,
+ form
+ use-template "StdUserObj" } ,
+ {
+ asn1 "Seq-descr.E.sp" ,
+ label "SWISS-PROT block" ,
+ prefix " " ,
+ form
+ use-template "StdSPBlock"} ,
+ {
+ asn1 "Seq-descr.E.neighbors" ,
+ label "Neighbors" ,
+ prefix " " ,
+ form
+ null NULL } ,
+ {
+ asn1 "Seq-descr.E.embl" ,
+ label "EMBL block" ,
+ prefix " " ,
+ form
+ null NULL } ,
+ {
+ asn1 "Seq-descr.E.create-date" ,
+ label "Create date" ,
+ prefix " " ,
+ form
+ user {
+ printfunc "StdDatePrint" } } ,
+ {
+ asn1 "Seq-descr.E.update-date" ,
+ label "Update date" ,
+ prefix " " ,
+ form
+ user {
+ printfunc "StdDatePrint" } } ,
+ {
+ asn1 "Seq-descr.E.prf" ,
+ label "PRF block" ,
+ prefix " " ,
+ form
+ null NULL } ,
+ {
+ asn1 "Seq-descr.E.pdb" ,
+ label "PDB block" ,
+ prefix " " ,
+ form
+ null NULL } ,
+ {
+ asn1 "Seq-descr.E.het" ,
+ label "Heterogen" ,
+ prefix " " ,
+ form
+ text {
+ } } } } } } ,
+ {
+ name "StdBioseqId" ,
+ format {
+ asn1 "Bioseq" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Bioseq.id" ,
+ prefix "" ,
+ suffix ";" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Bioseq.id.E.pir" ,
+ label "pir:" ,
+ prefix " " ,
+ form
+ use-template "StdPIRseqId" } ,
+ {
+ asn1 "Bioseq.id.E.other" ,
+ label "REFSEQ:" ,
+ prefix " " ,
+ form
+ use-template "StdOtherId" } ,
+ {
+ asn1 "Bioseq.id.E.local" ,
+ label "userid:" ,
+ prefix " " ,
+ form
+ use-template "StdLocalId" } ,
+ {
+ asn1 "Bioseq.id.E.genbank" ,
+ label "genbank:" ,
+ prefix " " ,
+ form
+ use-template "StdGPseqId" } ,
+ {
+ asn1 "Bioseq.id.E.swissprot" ,
+ label "swissprot:" ,
+ prefix " " ,
+ form
+ use-template "StdSPseqId" } ,
+ {
+ asn1 "Bioseq.id.E.prf" ,
+ label "prf:" ,
+ prefix " " ,
+ form
+ use-template "StdPRFseqId" } ,
+ {
+ asn1 "Bioseq.id.E.pdb" ,
+ label "pdb:" ,
+ prefix " " ,
+ form
+ use-template "StdPDBseqId" } } } } } } } } ,
+ {
+ name "VersionBioseqId" ,
+ format {
+ asn1 "Bioseq" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Bioseq.id" ,
+ prefix "" ,
+ suffix ";" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Bioseq.id.E.pir" ,
+ label "pir:" ,
+ prefix " " ,
+ form
+ use-template "StdPIRseqId" } ,
+ {
+ asn1 "Bioseq.id.E.local" ,
+ label "userid:" ,
+ prefix " " ,
+ form
+ use-template "StdLocalId" } ,
+ {
+ asn1 "Bioseq.id.E.genbank" ,
+ label "genbank:" ,
+ prefix " " ,
+ form
+ use-template "VersionGPseqId" } ,
+ {
+ asn1 "Bioseq.id.E.swissprot" ,
+ label "swissprot:" ,
+ prefix " " ,
+ form
+ use-template "StdSPseqId" } ,
+ {
+ asn1 "Bioseq.id.E.prf" ,
+ label "prf:" ,
+ prefix " " ,
+ form
+ use-template "StdPRFseqId" } ,
+ {
+ asn1 "Bioseq.id.E.pdb" ,
+ label "pdb:" ,
+ prefix " " ,
+ form
+ use-template "StdPDBseqId" } } } } } } } } ,
+ {
+ name "StdSeqFeatLocation" ,
+ format {
+ asn1 "Seq-feat.location" ,
+ label "Location" ,
+ prefix "\t" ,
+ form
+ user {
+ printfunc "StdSeqLocPrint" } } } ,
+ {
+ name "StdSeqFeatProduct" ,
+ format {
+ asn1 "Seq-feat.product" ,
+ label "Product" ,
+ prefix "\t" ,
+ form
+ user {
+ printfunc "StdSeqLocPrint" } } } ,
+ {
+ name "EntrySeqFeatData" ,
+ labelfrom "Seq-feat.data" ,
+ format {
+ asn1 "Seq-feat.data" ,
+ prefix "\t" ,
+ form
+ use-template "StdSeqFeatData" } } ,
+ {
+ name "StdSeqFeat" ,
+ labelfrom "Seq-feat.data" ,
+ format {
+ asn1 "Seq-feat" ,
+ prefix " " ,
+ suffix " " ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Seq-feat.data" ,
+ form
+ use-template "StdSeqFeatData" } ,
+ {
+ asn1 "Seq-feat" ,
+ form
+ use-template "StdSeqFeatCommon" } ,
+ {
+ asn1 "Seq-feat.product" ,
+ label "Product" ,
+ prefix " " ,
+ form
+ user {
+ printfunc "StdSeqLocPrint" } } ,
+ {
+ asn1 "Seq-feat.location" ,
+ label "Location" ,
+ prefix " " ,
+ form
+ user {
+ printfunc "StdSeqLocPrint" } } ,
+ {
+ asn1 "Seq-feat.cit" ,
+ label "Citations" ,
+ prefix " " ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Seq-feat.cit.pub.E" ,
+ form
+ use-template "StdPub" } } } } ,
+ {
+ asn1 "Seq-feat.xref" ,
+ label "Cross-reference" ,
+ prefix " " ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Seq-feat.xref.E" ,
+ form
+ use-template "StdSeqFeatXref" } } } } } } } } ,
+ {
+ name "StdSeqFeatData" ,
+ format {
+ asn1 "SeqFeatData" ,
+ form
+ block {
+ components {
+ {
+ asn1 "SeqFeatData.gene" ,
+ label "Gene" ,
+ form
+ use-template "StdGeneRef" } ,
+ {
+ asn1 "SeqFeatData.org" ,
+ label "Organism" ,
+ form
+ use-template "StdOrgRef" } ,
+ {
+ asn1 "SeqFeatData.cdregion" ,
+ label "Coding Region" ,
+ form
+ use-template "StdCdRegion" } ,
+ {
+ asn1 "SeqFeatData.prot" ,
+ label "Protein" ,
+ form
+ use-template "StdProtRef" } ,
+ {
+ asn1 "SeqFeatData.rna" ,
+ label "RNA" ,
+ form
+ use-template "StdRNARef" } ,
+ {
+ asn1 "SeqFeatData.pub" ,
+ label "Citation" ,
+ form
+ use-template "StdPubdesc" } ,
+ {
+ asn1 "SeqFeatData.seq" ,
+ label "Sequence" ,
+ form
+ user {
+ printfunc "StdSeqLocPrint" } } ,
+ {
+ asn1 "SeqFeatData.imp.key" ,
+ label "Import" ,
+ form
+ use-template "StdImpFeat" } ,
+ {
+ asn1 "SeqFeatData.region" ,
+ label "Region" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "SeqFeatData.comment" ,
+ label "Comment" ,
+ form
+ null NULL } ,
+ {
+ asn1 "SeqFeatData.bond" ,
+ label "Bond" ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "SeqFeatData.site" ,
+ label "Site" ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "SeqFeatData.rsite" ,
+ label "Rest. Site" ,
+ form
+ use-template "StdRsiteRef" } ,
+ {
+ asn1 "SeqFeatData.user" ,
+ label "User Type" ,
+ form
+ use-template "StdUserObj" } ,
+ {
+ asn1 "SeqFeatData.txinit" ,
+ label "TxInit" ,
+ form
+ use-template "StdTxInit" } ,
+ {
+ asn1 "SeqFeatData.num" ,
+ label "Numbering" ,
+ form
+ use-template "StdNumbering" } ,
+ {
+ asn1 "SeqFeatData.psec-str" ,
+ label "Sec. Struct" ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "SeqFeatData.non-std-residue" ,
+ label "NonStd Residue" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "SeqFeatData.het" ,
+ label "Heterogen" ,
+ form
+ text {
+ } } } } } } ,
+ {
+ name "StdGeneRef" ,
+ format {
+ asn1 "Gene-ref" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Gene-ref" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Gene-ref.locus" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Gene-ref.allele" ,
+ prefix " " ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "Gene-ref.desc" ,
+ prefix "[" ,
+ suffix "]" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Gene-ref.pseudo" ,
+ form
+ boolean {
+ true "This is a pseudogene." } } ,
+ {
+ asn1 "Gene-ref.syn" ,
+ label "Synonyms" ,
+ prefix " (" ,
+ suffix ")" ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Gene-ref.syn.E" ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "Gene-ref.maploc" ,
+ label "Map Location" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Gene-ref.db" ,
+ label "Cross Reference" ,
+ prefix " " ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Gene-ref.db.E" ,
+ prefix "(" ,
+ suffix ")" ,
+ form
+ use-template "StdDbtag" } } } } } } } } ,
+ {
+ name "StdUserObj" ,
+ format {
+ asn1 "User-object" ,
+ label "User-object" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "User-object.class" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "User-object.type" ,
+ form
+ use-template "StdObjectId" } } } } } ,
+ {
+ name "StdSPBlock" ,
+ format {
+ asn1 "SP-block" ,
+ prefix "" ,
+ suffix " " ,
+ form
+ block {
+ separator ";~" ,
+ components {
+ {
+ asn1 "SP-block.class" ,
+ label "class: " ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "SP-block.extra-acc" ,
+ label "extra accessions:" ,
+ prefix " " ,
+ form
+ block {
+ separator ", ",
+ components {
+ {
+ asn1 "SP-block.extra-acc.E" ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "SP-block.imeth" ,
+ form
+ boolean {
+ true "seq starts with Met" } } ,
+ {
+ asn1 "SP-block.plasnm" ,
+ prefix " " ,
+ form
+ block {
+ separator ", ",
+ components {
+ {
+ asn1 "SP-block.plasnm.E" ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "SP-block.seqref" ,
+ label "xrefs:" ,
+ prefix " " ,
+ form
+ block {
+ separator ", ",
+ components {
+ {
+ asn1 "Seq-id.local" ,
+ form
+ use-template "StdObjectId" } ,
+ {
+ asn1 "Seq-id.genbank" ,
+ label "genbank" ,
+ prefix " " ,
+ form
+ use-template "StdTextseqId" } ,
+ {
+ asn1 "Seq-id.embl" ,
+ label "embl" ,
+ prefix " " ,
+ form
+ use-template "StdEMBLseqId" } ,
+ {
+ asn1 "Seq-id.pir" ,
+ label "pir" ,
+ prefix " " ,
+ form
+ use-template "StdTextseqId" } ,
+ {
+ asn1 "Seq-id.swissprot" ,
+ label "swissprot" ,
+ prefix " " ,
+ form
+ use-template "StdTextseqId" } ,
+ {
+ asn1 "Seq-id.patent" ,
+ form
+ use-template "StdPatentSeqId" } ,
+ {
+ asn1 "Seq-id.other" ,
+ label "REFSEQ:" ,
+ prefix " " ,
+ form
+ use-template "StdTextseqId" } ,
+ {
+ asn1 "Seq-id.general" ,
+ form
+ use-template "StdDbtag" } ,
+ {
+ asn1 "Seq-id.gi" ,
+ label "gi:" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Seq-id.ddbj" ,
+ label "ddbj" ,
+ prefix " " ,
+ form
+ use-template "StdTextseqId" } ,
+ {
+ asn1 "Seq-id.prf" ,
+ label "prf" ,
+ prefix " " ,
+ form
+ use-template "StdTextseqId" } ,
+ {
+ asn1 "Seq-id.pdb" ,
+ form
+ use-template "StdPDBseqId" } ,
+ } } } ,
+ {
+ asn1 "SP-block.dbref" ,
+ label "xrefs (non-sequence databases):" ,
+ prefix " " ,
+ form
+ block {
+ separator ", ",
+ components {
+ {
+ asn1 "SP-block.dbref.E" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Dbtag.db" ,
+ suffix ": " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Dbtag.tag" ,
+ form
+ use-template "StdObjectId" } ,
+ } } } } } } ,
+ {
+ asn1 "SP-block.created" ,
+ label "created:" ,
+ prefix " " ,
+ form
+ user {
+ printfunc "StdDatePrint" } } ,
+ {
+ asn1 "SP-block.sequpd" ,
+ label "sequence updated:" ,
+ prefix " " ,
+ form
+ user {
+ printfunc "StdDatePrint" } } ,
+ {
+ asn1 "SP-block.annotupd" ,
+ label "annotation updated:" ,
+ prefix " " ,
+ form
+ user {
+ printfunc "StdDatePrint" } } ,
+ } } } } ,
+ {
+ name "StdPirBlock" ,
+ format {
+ asn1 "PIR-block" ,
+ prefix "" ,
+ suffix "" ,
+ form
+ block {
+ separator ";~" ,
+ components {
+ {
+ asn1 "PIR-block.host" ,
+ label "host:" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "PIR-block.source" ,
+ label "source: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "PIR-block.summary" ,
+ label "summary: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "PIR-block.genetic" ,
+ label "genetic: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "PIR-block.includes" ,
+ label "includes: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "PIR-block.placement" ,
+ label "placement: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "PIR-block.superfamily" ,
+ label "superfamily: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "PIR-block.cross-reference" ,
+ label "xref: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "PIR-block.date" ,
+ label "PIR dates: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "PIR-block.had-punct" ,
+ form
+ boolean {
+ true "punctuation in sequence" } } ,
+ {
+ asn1 "PIR-block.seqref" ,
+ label "xrefs:" ,
+ prefix " " ,
+ form
+ block {
+ separator ", ",
+ components {
+ {
+ asn1 "Seq-id.local" ,
+ form
+ use-template "StdObjectId" } ,
+ {
+ asn1 "Seq-id.genbank" ,
+ label "genbank" ,
+ form
+ use-template "StdTextseqId" } ,
+ {
+ asn1 "Seq-id.embl" ,
+ label "embl" ,
+ prefix " " ,
+ form
+ use-template "StdEMBLseqId" } ,
+ {
+ asn1 "Seq-id.pir" ,
+ label "pir" ,
+ prefix " " ,
+ form
+ use-template "StdTextseqId" } ,
+ {
+ asn1 "Seq-id.swissprot" ,
+ label "swissprot" ,
+ prefix " " ,
+ form
+ use-template "StdTextseqId" } ,
+ {
+ asn1 "Seq-id.patent" ,
+ form
+ use-template "StdPatentSeqId" } ,
+ {
+ asn1 "Seq-id.other" ,
+ form
+ use-template "StdTextseqId" } ,
+ {
+ asn1 "Seq-id.general" ,
+ form
+ null NULL } ,
+ {
+ asn1 "Seq-id.gi" ,
+ label "gi:" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Seq-id.ddbj" ,
+ label "ddbj" ,
+ prefix " " ,
+ form
+ use-template "StdTextseqId" } ,
+ {
+ asn1 "Seq-id.prf" ,
+ label "prf" ,
+ prefix " " ,
+ form
+ use-template "StdTextseqId" } ,
+ {
+ asn1 "Seq-id.pdb" ,
+ form
+ use-template "StdPDBseqId" } ,
+ } } } ,
+ } } } } ,
+ {
+ name "StdPDBBlock" ,
+ format {
+ asn1 "PDB-block" ,
+ prefix "" ,
+ suffix "" ,
+ form
+ block {
+ separator ";~" ,
+ components {
+ {
+ asn1 "PDB-block.deposition" ,
+ label "deposition: " ,
+ form
+ user {
+ printfunc "StdDatePrint" } } ,
+ {
+ asn1 "PDB-block.class" ,
+ label "class: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "PDB-block.source" ,
+ label "source:" ,
+ prefix " " ,
+ form
+ block {
+ separator ", ",
+ components {
+ {
+ asn1 "PDB-block.source.E" ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "PDB-block.exp-method" ,
+ label "Non X-ray method: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "PDB-block.replace" ,
+ prefix "" ,
+ form
+ use-template "Pdb-replace" } ,
+ } } } } ,
+ {
+ name "Pdb-replace" ,
+ format {
+ asn1 "PDB-replace" ,
+ prefix "" ,
+ suffix "" ,
+ form
+ block {
+ separator ";~" ,
+ components {
+ {
+ asn1 "PDB-replace.date" ,
+ label "replacement date:" ,
+ prefix " " ,
+ form
+ user {
+ printfunc "StdDatePrint" } } ,
+ {
+ asn1 "PDB-replace.ids" ,
+ label "ids replaced:" ,
+ prefix " " ,
+ form
+ block {
+ separator ", ",
+ components {
+ {
+ asn1 "PDB-replace.ids.E" ,
+ form
+ text {
+ } } } } } ,
+ } } } } ,
+ {
+ name "StdPRFBlock" ,
+ format {
+ asn1 "PRF-block" ,
+ prefix "" ,
+ suffix "" ,
+ form
+ block {
+ separator ";~" ,
+ components {
+ {
+ asn1 "PRF-block.extra-src" ,
+ prefix "" ,
+ form
+ use-template "Prf-Extra-src" } ,
+ } } } } ,
+ {
+ name "Prf-Extra-src" ,
+ format {
+ asn1 "PRF-ExtraSrc" ,
+ prefix "" ,
+ suffix "" ,
+ form
+ block {
+ separator ";~" ,
+ components {
+ {
+ asn1 "PRF-ExtraSrc.host" ,
+ label "host:" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "PRF-ExtraSrc.part" ,
+ label "part:" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "PRF-ExtraSrc.state" ,
+ label "state:" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "PRF-ExtraSrc.strain" ,
+ label "strain:" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "PRF-ExtraSrc.taxon" ,
+ label "taxonomy:" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ } } } } ,
+ {
+ name "StdSPBXRef" ,
+ format {
+ asn1 "SP-block" ,
+ prefix " " ,
+ suffix " " ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "SP-block.seqref" ,
+ prefix " " ,
+ form
+ block {
+ separator ", ",
+ components {
+ {
+ asn1 "Seq-id.local" ,
+ form
+ use-template "StdObjectId" } ,
+ {
+ asn1 "Seq-id.genbank" ,
+ label "genbank" ,
+ form
+ use-template "StdTextseqId" } ,
+ {
+ asn1 "Seq-id.embl" ,
+ label "embl" ,
+ prefix " " ,
+ form
+ use-template "StdEMBLseqId" } ,
+ {
+ asn1 "Seq-id.pir" ,
+ label "pir" ,
+ prefix " " ,
+ form
+ use-template "StdTextseqId" } ,
+ {
+ asn1 "Seq-id.swissprot" ,
+ label "swissprot" ,
+ prefix " " ,
+ form
+ use-template "StdTextseqId" } ,
+ {
+ asn1 "Seq-id.patent" ,
+ form
+ use-template "StdPatentSeqId" } ,
+ {
+ asn1 "Seq-id.other" ,
+ form
+ use-template "StdTextseqId" } ,
+ {
+ asn1 "Seq-id.general" ,
+ form
+ null NULL } ,
+ {
+ asn1 "Seq-id.gi" ,
+ label "gi:" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Seq-id.ddbj" ,
+ label "ddbj" ,
+ prefix " " ,
+ form
+ use-template "StdTextseqId" } ,
+ {
+ asn1 "Seq-id.prf" ,
+ label "prf" ,
+ prefix " " ,
+ form
+ use-template "StdTextseqId" } ,
+ {
+ asn1 "Seq-id.pdb" ,
+ form
+ use-template "StdPDBseqId" } ,
+ } } } ,
+ } } } } ,
+ {
+ name "StdPub" ,
+ format {
+ asn1 "Pub" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Pub.gen" ,
+ form
+ use-template "StdCitGen" } ,
+ {
+ asn1 "Pub.sub" ,
+ form
+ use-template "StdCitSub" } ,
+ {
+ asn1 "Pub.medline" ,
+ form
+ use-template "StdMedlineEntry" } ,
+ {
+ asn1 "Pub.muid" ,
+ label "MEDLINE uid: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Pub.article" ,
+ form
+ use-template "StdCitArt" } ,
+ {
+ asn1 "Pub.journal" ,
+ form
+ use-template "StdCitJour" } ,
+ {
+ asn1 "Pub.book" ,
+ form
+ use-template "StdCitBook" } ,
+ {
+ asn1 "Pub.proc" ,
+ form
+ use-template "StdCitProc" } ,
+ {
+ asn1 "Pub.patent" ,
+ form
+ use-template "StdCitPat" } ,
+ {
+ asn1 "Pub.pat-id" ,
+ form
+ use-template "StdIdPat" } ,
+ {
+ asn1 "Pub.man" ,
+ form
+ use-template "StdCitLet" } ,
+ {
+ asn1 "Pub.equiv" ,
+ form
+ use-template "StdPubEquiv" } } } } } ,
+ {
+ name "StdCitGen" ,
+ format {
+ asn1 "Cit-gen" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Cit-gen.serial-number" ,
+ prefix "[" ,
+ suffix "]" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cit-gen.authors" ,
+ form
+ use-template "StdAuthList" } ,
+ {
+ asn1 "Cit-gen.date" ,
+ prefix "(" ,
+ suffix ")" ,
+ form
+ user {
+ printfunc "StdDatePrint" } } ,
+ {
+ asn1 "Cit-gen.title" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cit-gen.cit" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cit-gen" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Cit-gen.journal" ,
+ suffix ":" ,
+ form
+ use-template "StdTitle" } ,
+ {
+ asn1 "Cit-gen.issue" ,
+ suffix ";" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cit-gen.pages" ,
+ form
+ text {
+ } } } } } } } } } ,
+ {
+ name "StdCitSub" ,
+ format {
+ asn1 "Cit-sub" ,
+ prefix "Data Submission " ,
+ form
+ block {
+ components {
+ {
+ asn1 "Cit-sub.medium" ,
+ prefix "on " ,
+ suffix " " ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "Cit-sub.imp.date" ,
+ prefix "(" ,
+ suffix ")" ,
+ form
+ user {
+ printfunc "StdDatePrint" } } ,
+ {
+ asn1 "Cit-sub.authors" ,
+ prefix " " ,
+ form
+ use-template "StdAuthList" } } } } } ,
+ {
+ name "StdMedlineEntry" ,
+ format {
+ asn1 "Medline-entry" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Medline-entry" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Medline-entry.uid" ,
+ label "uid" ,
+ prefix ": " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Medline-entry.em" ,
+ label "entry month" ,
+ prefix ": " ,
+ form
+ user {
+ printfunc "StdDatePrint" } } } } } ,
+ {
+ asn1 "Medline-entry.cit" ,
+ form
+ use-template "StdCitArt" } ,
+ {
+ asn1 "Medline-entry.abstract" ,
+ label "abstract" ,
+ prefix ": " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Medline-entry.mesh" ,
+ label "Mesh Terms" ,
+ prefix " " ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Medline-entry.mesh.E" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Medline-mesh.term" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Medline-mesh.mp" ,
+ form
+ boolean {
+ true " (Main Point)" } } ,
+ {
+ asn1 "Medline-mesh.qual" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Medline-mesh.qual.E" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Medline-qual.subh" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Medline-qual.mp" ,
+ form
+ boolean {
+ true " (Main Point)" } } } } } } } } } } } } } } ,
+ {
+ asn1 "Medline-entry.substance" ,
+ label "Substance" ,
+ prefix " " ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Medline-entry.substance.E" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Medline-rn.name" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Medline-rn.type" ,
+ form
+ enum {
+ values {
+ "" ,
+ " CAS: " ,
+ "EC " } } } ,
+ {
+ asn1 "Medline-rn.cit" ,
+ form
+ text {
+ } } } } } } } } ,
+ {
+ asn1 "Medline-entry.xref" ,
+ label "Cross Reference" ,
+ prefix " " ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Medline-entry.xref.E" ,
+ form
+ block {
+ separator ": " ,
+ components {
+ {
+ asn1 "Medline-si.type" ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "Medline-si.cit" ,
+ form
+ text {
+ } } } } } } } } ,
+ {
+ asn1 "Medline-entry.gene" ,
+ label "Possible Gene Symbols" ,
+ prefix ": " ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Medline-entry.gene.E" ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "Medline-entry.idnum" ,
+ label "Support" ,
+ prefix ": " ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Medline-entry.idnum.E" ,
+ form
+ text {
+ } } } } } } } } } ,
+ {
+ name "StdCitArt" ,
+ format {
+ asn1 "Cit-art" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Cit-art.title" ,
+ form
+ use-template "StdTitle" } ,
+ {
+ asn1 "Cit-art.authors" ,
+ form
+ use-template "StdAuthList" } ,
+ {
+ asn1 "Cit-art.from.journal" ,
+ form
+ use-template "StdCitJour" } ,
+ {
+ asn1 "Cit-art.from.book" ,
+ prefix "(in) " ,
+ form
+ use-template "StdCitBook" } ,
+ {
+ asn1 "Cit-art.from.proc" ,
+ prefix "(in) " ,
+ form
+ use-template "StdCitProc" } } } } } ,
+ {
+ name "StdCitJour" ,
+ format {
+ asn1 "Cit-jour" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Cit-jour.title" ,
+ form
+ use-template "StdTitle" } ,
+ {
+ asn1 "Cit-jour.imp" ,
+ form
+ use-template "StdImprint" } } } } } ,
+ {
+ name "StdCitBook" ,
+ format {
+ asn1 "Cit-book" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Cit-book.title" ,
+ form
+ use-template "StdTitle" } ,
+ {
+ asn1 "Cit-book.coll" ,
+ prefix "Collection: " ,
+ form
+ use-template "StdTitle" } ,
+ {
+ asn1 "Cit-book.authors" ,
+ form
+ use-template "StdAuthList" } ,
+ {
+ asn1 "Cit-book.imp" ,
+ form
+ use-template "StdImprint" } } } } } ,
+ {
+ name "StdCitProc" ,
+ format {
+ asn1 "Cit-proc" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Cit-proc.book" ,
+ form
+ use-template "StdCitBook" } ,
+ {
+ asn1 "Cit-proc.meet" ,
+ label "Meeting " ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Meeting.number" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Meeting.date" ,
+ form
+ user {
+ printfunc "StdDatePrint" } } ,
+ {
+ asn1 "Meeting.place" ,
+ form
+ use-template "StdAffil" } } } } } } } } ,
+ {
+ name "StdCitPat" ,
+ format {
+ asn1 "Cit-pat" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Cit-pat.title" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cit-pat.authors" ,
+ form
+ use-template "StdAuthList" } ,
+ {
+ asn1 "Cit-pat" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Cit-pat.country" ,
+ suffix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cit-pat.doc-type" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cit-pat.number" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cit-pat.date-issue" ,
+ prefix " (" ,
+ suffix ")" ,
+ form
+ user {
+ printfunc "StdDatePrint" } } ,
+ {
+ asn1 "Cit-pat.app-number" ,
+ prefix " Appl: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cit-pat.app-date" ,
+ prefix " (" ,
+ suffix ")" ,
+ form
+ user {
+ printfunc "StdDatePrint" } } } } } } } } } ,
+ {
+ name "StdIdPat" ,
+ format {
+ asn1 "Id-pat" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Id-pat.country" ,
+ suffix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Id-pat.id.number" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Id-pat.id.app-number" ,
+ prefix "Appl: " ,
+ form
+ text {
+ } } } } } } ,
+ {
+ name "StdPatentSeqId" ,
+ format {
+ asn1 "Patent-seq-id" ,
+ label "patent: " ,
+ form
+ block {
+ components {
+ {
+ asn1 "Patent-seq-id.seqid" ,
+ suffix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Patent-seq-id.cit" ,
+ prefix " " ,
+ form
+ use-template "StdIdPat" } } } } } ,
+ {
+ name "StdCitLet" ,
+ format {
+ asn1 "Cit-let" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Cit-let.type" ,
+ prefix "[" ,
+ suffix "]" ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "Cit-let.man-id" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cit-let.cit" ,
+ form
+ use-template "StdCitBook" } } } } } ,
+ {
+ name "StdPubEquiv" ,
+ format {
+ asn1 "Pub-equiv" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Pub-equiv.E" ,
+ form
+ use-template "StdPub" } } } } } ,
+ {
+ name "StdTitle" ,
+ format {
+ asn1 "Title" ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Title.E.trans" ,
+ prefix "[" ,
+ suffix "]" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Title.E.name" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Title.E.tsub" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Title.E.abr" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Title.E.iso-jta" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Title.E.ml-jta" ,
+ label "MEDLINE" ,
+ prefix ": " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Title.E.jta" ,
+ label "jta" ,
+ prefix ": " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Title.E.issn" ,
+ label "ISSN" ,
+ prefix ": " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Title.E.coden" ,
+ label "CODEN" ,
+ prefix ": " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Title.E.isbn" ,
+ label "ISBN" ,
+ prefix ": " ,
+ form
+ text {
+ } } } } } } ,
+ {
+ name "StdAuthList" ,
+ format {
+ asn1 "Auth-list" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Auth-list" ,
+ form
+ user {
+ printfunc "StdAuthListNamesPrint" } } ,
+ {
+ asn1 "Auth-list.affil" ,
+ form
+ use-template "StdAffil" } } } } } ,
+ {
+ name "StdAffil" ,
+ format {
+ asn1 "Affil" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Affil.str" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Affil.std.affil" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Affil.std.div" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Affil.std.street" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Affil.std" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Affil.std.city" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Affil.std.sub" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Affil.std.country" ,
+ form
+ text {
+ } } } } } } } } } ,
+ {
+ name "StdImprint" ,
+ format {
+ asn1 "Imprint" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Imprint.date" ,
+ prefix "(" ,
+ suffix ") " ,
+ form
+ user {
+ printfunc "StdDatePrint" } } ,
+ {
+ asn1 "Imprint.volume" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Imprint.issue" ,
+ prefix " (" ,
+ suffix ")" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Imprint.section" ,
+ prefix " (" ,
+ suffix ")" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Imprint.part-sup" ,
+ prefix " (" ,
+ suffix ")" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Imprint.pages" ,
+ prefix ": " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Imprint.prepub" ,
+ prefix " (" ,
+ suffix ")" ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "Imprint.pub" ,
+ label " Publisher: " ,
+ form
+ use-template "StdAffil" } ,
+ {
+ asn1 "Imprint.cprt" ,
+ label " Copyright: " ,
+ form
+ user {
+ printfunc "StdDatePrint" } } } } } } ,
+ {
+ name "StdSeqFeatXref" ,
+ format {
+ asn1 "SeqFeatXref" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "SeqFeatXref.id" ,
+ label "Id=" ,
+ form
+ use-template "StdFeatId" } ,
+ {
+ asn1 "SeqFeatXref.data" ,
+ form
+ use-template "StdSeqFeatData" } } } } } ,
+ {
+ name "StdOrgRef" ,
+ format {
+ asn1 "Org-ref" ,
+ label "Org-ref" ,
+ prefix " " ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Org-ref" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Org-ref.taxname" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Org-ref.common" ,
+ prefix "(" ,
+ suffix ")" ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "Org-ref.mod" ,
+ label "Modifiers" ,
+ prefix " (" ,
+ suffix ")" ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Org-ref.mod.E" ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "Org-ref.db" ,
+ label "Cross Reference" ,
+ prefix " " ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Org-ref.db.E" ,
+ prefix "(" ,
+ suffix ")" ,
+ form
+ use-template "StdDbtag" } } } } ,
+ {
+ asn1 "Org-ref.syn" ,
+ label "Synonyms" ,
+ prefix " (" ,
+ suffix ")" ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Org-ref.syn.E" ,
+ form
+ text {
+ } } } } } } } } } ,
+ {
+ name "StdCdRegion" ,
+ format {
+ asn1 "Cdregion" ,
+ label "Cdregion" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Cdregion.orf" ,
+ form
+ boolean {
+ true "Uncharacterized Open Reading Frame" } } ,
+ {
+ asn1 "Cdregion.frame" ,
+ label "Reading Frame = " ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "Cdregion.code" ,
+ label "Genetic Code: " ,
+ suffix ";" ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Genetic-code.E.name" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Genetic-code.E.id" ,
+ label "id= " ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "Cdregion.conflict" ,
+ form
+ boolean {
+ true "Translation conflicts with protein sequence" } } ,
+ {
+ asn1 "Cdregion.stops" ,
+ prefix "Translation contains " ,
+ suffix " stop codons" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cdregion.gaps" ,
+ prefix "Translation contains " ,
+ suffix " gaps when aligned to protein" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cdregion.mismatch" ,
+ prefix "Translation contains " ,
+ suffix " mismatches when aligned to protein" ,
+ form
+ text {
+ } } } } } } ,
+ {
+ name "StdProtRef" ,
+ format {
+ asn1 "Prot-ref" ,
+ label "Prot-ref" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Prot-ref.name" ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Prot-ref.name.E" ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "Prot-ref.desc" ,
+ prefix "[" ,
+ suffix "]" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Prot-ref.ec" ,
+ label "ec" ,
+ prefix ": " ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Prot-ref.ec.E" ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "Prot-ref.activity" ,
+ label "activity" ,
+ prefix ": " ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Prot-ref.activity.E" ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "Prot-ref.db" ,
+ form
+ use-template "StdDbtag" } } } } } ,
+ {
+ name "StdRNARef" ,
+ format {
+ asn1 "RNA-ref" ,
+ label "RNA-ref" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "RNA-ref.type" ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "RNA-ref.pseudo" ,
+ form
+ boolean {
+ true "This is an RNA pseudogene." } } ,
+ {
+ asn1 "RNA-ref.ext.name" ,
+ form
+ text {
+ } } } } } } ,
+ {
+ name "StdPubdesc" ,
+ format {
+ asn1 "Pubdesc" ,
+ label "Pubdesc" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Pubdesc.pub" ,
+ form
+ use-template "StdPubEquiv" } ,
+ {
+ asn1 "Pubdesc" ,
+ prefix "In this article: " ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Pubdesc.name" ,
+ label "name=" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Pubdesc.fig" ,
+ label "figure=" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Pubdesc.poly-a" ,
+ form
+ boolean {
+ true "poly(A) shown" } } ,
+ {
+ asn1 "Pubdesc.maploc" ,
+ label "map location=" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Pubdesc.num" ,
+ form
+ use-template "StdNumbering" } ,
+ {
+ asn1 "Pubdesc.numexc" ,
+ form
+ boolean {
+ true "numbering inconsistent" } } } } } ,
+ {
+ asn1 "Pubdesc.comment" ,
+ form
+ text {
+ } } } } } } ,
+ {
+ name "StdImpFeat" ,
+ format {
+ asn1 "Imp-feat.key" ,
+ label "Imp-feat" ,
+ form
+ text {
+ } } } ,
+ {
+ name "StdRsiteRef" ,
+ format {
+ asn1 "Rsite-ref" ,
+ label "Rsite-ref" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Rsite-ref.str" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Rsite-ref.std" ,
+ form
+ use-template "StdDbtag" } } } } } ,
+ {
+ name "StdTxInit" ,
+ format {
+ asn1 "TxInit" ,
+ label "TxInit" ,
+ form
+ null NULL } } ,
+ {
+ name "StdNumbering" ,
+ format {
+ asn1 "Numbering" ,
+ label "Numbering" ,
+ form
+ null NULL } } ,
+ {
+ name "StdFeatId" ,
+ format {
+ asn1 "Feat-id" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Feat-id.gibb" ,
+ label "GenInfo Backbone: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Feat-id.giim.id" ,
+ label "GenInfo Import Id: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Feat-id.local" ,
+ label "Local: " ,
+ form
+ use-template "StdObjectId" } ,
+ {
+ asn1 "Feat-id.general" ,
+ form
+ use-template "StdDbtag" } } } } } ,
+ {
+ name "StdSeqFeatCommon" ,
+ format {
+ asn1 "Seq-feat" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Seq-feat.id" ,
+ label "Id=" ,
+ form
+ use-template "StdFeatId" } ,
+ {
+ asn1 "Seq-feat.title" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Seq-feat" ,
+ suffix ";" ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Seq-feat.partial" ,
+ form
+ boolean {
+ true "Partial" } } ,
+ {
+ asn1 "Seq-feat.except" ,
+ form
+ boolean {
+ true "Biological Exception" } } ,
+ {
+ asn1 "Seq-feat.exp-ev" ,
+ label "Evidence" ,
+ prefix " is " ,
+ form
+ enum {
+ } } } } } ,
+ {
+ asn1 "Seq-feat.comment" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Seq-feat.ext" ,
+ form
+ use-template "StdUserObj" } ,
+ {
+ asn1 "Seq-feat.qual" ,
+ label "Qualifiers" ,
+ prefix " " ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Seq-feat.qual.E" ,
+ prefix "\\" ,
+ form
+ block {
+ separator "= " ,
+ components {
+ {
+ asn1 "Gb-qual.qual" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Gb-qual.val" ,
+ form
+ text {
+ } } } } } } } } } } } } ,
+ {
+ name "StdDbtag" ,
+ format {
+ asn1 "Dbtag" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Dbtag.db" ,
+ suffix ": " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Dbtag.tag" ,
+ form
+ use-template "StdObjectId" } } } } } ,
+ {
+ name "StdObjectId" ,
+ format {
+ asn1 "Object-id" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Object-id.id" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Object-id.str" ,
+ form
+ text {
+ } } } } } } ,
+ {
+ name "StdTextseqId" ,
+ format {
+ asn1 "Textseq-id" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Textseq-id.name" ,
+ label "locus" ,
+ prefix " " ,
+ suffix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Textseq-id.accession" ,
+ label "accession" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Textseq-id.release" ,
+ label "release" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Textseq-id.version" ,
+ label "" ,
+ form
+ text {
+ } } } } } } ,
+ {
+ name "VersionTextseqId" ,
+ format {
+ asn1 "Textseq-id" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Textseq-id.name" ,
+ label "locus" ,
+ prefix " " ,
+ suffix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Textseq-id.accession" ,
+ label "accession" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Textseq-id.release" ,
+ label "release" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Textseq-id.version" ,
+ label "." ,
+ prefix "" ,
+ form
+ text {
+ } } } } } } ,
+ {
+ name "StdPDBseqId" ,
+ format {
+ asn1 "PDB-seq-id" ,
+ label "PDB Id: " ,
+ form
+ block {
+ components {
+ {
+ asn1 "PDB-seq-id.mol" ,
+ label "molecule" ,
+ prefix " " ,
+ suffix ", " ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "PDB-mol-id" ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "PDB-seq-id.chain" ,
+ label "chain" ,
+ prefix " " ,
+ suffix ", " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "PDB-seq-id.rel" ,
+ label "release" ,
+ prefix " " ,
+ form
+ user {
+ printfunc "StdDatePrint" } } } } } } ,
+ {
+ name "StdEMBLseqId" ,
+ format {
+ asn1 "Textseq-id" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Textseq-id.name" ,
+ label "locus" ,
+ prefix " " ,
+ suffix ", " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Textseq-id.accession" ,
+ label "accession" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Textseq-id.release" ,
+ label "release" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Textseq-id.version" ,
+ label "." ,
+ prefix "" ,
+ form
+ text {
+ } } ,
+ } } } } ,
+ {
+ name "StdPIRseqId" ,
+ format {
+ asn1 "Textseq-id" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Textseq-id.name" ,
+ label "locus" ,
+ prefix " " ,
+ suffix "" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Textseq-id.accession" ,
+ label " accession" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ } } } } ,
+ {
+ name "StdPRFseqId" ,
+ format {
+ asn1 "Textseq-id" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Textseq-id.name" ,
+ label "locus" ,
+ prefix " " ,
+ suffix "" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Textseq-id.accession" ,
+ label " accession" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ } } } } ,
+ {
+ name "StdPDBseqId" ,
+ format {
+ asn1 "Textseq-id" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Textseq-id.name" ,
+ label "locus" ,
+ prefix " " ,
+ suffix "" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Textseq-id.accession" ,
+ label " accession" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ } } } } ,
+ {
+ name "StdSPseqId" ,
+ format {
+ asn1 "Textseq-id" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Textseq-id.name" ,
+ label "locus" ,
+ prefix " " ,
+ suffix "," ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Textseq-id.accession" ,
+ label " accession" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ } } } } ,
+ {
+ name "StdLocalId" ,
+ format {
+ asn1 "Object-id" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Object-id.id" ,
+ prefix " " ,
+ suffix "" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Object-id.str" ,
+ prefix " " ,
+ suffix "" ,
+ form
+ text {
+ } } } } } } ,
+ {
+ name "StdOtherId" ,
+ format {
+ asn1 "Textseq-id" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Textseq-id.name" ,
+ label "locus" ,
+ prefix " " ,
+ suffix "," ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Textseq-id.accession" ,
+ label " accession" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ } } } } ,
+ {
+ name "StdGPseqId" ,
+ format {
+ asn1 "Textseq-id" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Textseq-id.name" ,
+ label "locus" ,
+ prefix " " ,
+ suffix "," ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Textseq-id.accession" ,
+ label " accession" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ } } } } ,
+ {
+ name "StdSeqId" ,
+ format {
+ asn1 "Seq-id" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Seq-id.local" ,
+ form
+ use-template "StdObjectId" } ,
+ {
+ asn1 "Seq-id.genbank" ,
+ form
+ use-template "StdTextseqId" } ,
+ {
+ asn1 "Seq-id.embl" ,
+ label "embl" ,
+ prefix " " ,
+ form
+ use-template "StdEMBLseqId" } ,
+ {
+ asn1 "Seq-id.pir" ,
+ label "pir" ,
+ prefix " " ,
+ form
+ use-template "StdTextseqId" } ,
+ {
+ asn1 "Seq-id.swissprot" ,
+ form
+ use-template "StdTextseqId" } ,
+ {
+ asn1 "Seq-id.patent" ,
+ form
+ use-template "StdPatentSeqId" } ,
+ {
+ asn1 "Seq-id.other" ,
+ label "REFSEQ:" ,
+ prefix " " ,
+ form
+ use-template "StdTextseqId" } ,
+ {
+ asn1 "Seq-id.general" ,
+ form
+ null NULL } ,
+ {
+ asn1 "Seq-id.gi" ,
+ label "gi:" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Seq-id.ddbj" ,
+ form
+ use-template "StdTextseqId" } ,
+ {
+ asn1 "Seq-id.prf" ,
+ form
+ use-template "StdTextseqId" } ,
+ {
+ asn1 "Seq-id.pdb" ,
+ form
+ use-template "StdPDBseqId" } ,
+ }
+ } } } ,
+ {
+ name "VersionSeqId" ,
+ format {
+ asn1 "Seq-id" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Seq-id.local" ,
+ form
+ use-template "StdObjectId" } ,
+ {
+ asn1 "Seq-id.genbank" ,
+ form
+ use-template "VersionTextseqId" } ,
+ {
+ asn1 "Seq-id.embl" ,
+ label "embl" ,
+ prefix " " ,
+ form
+ use-template "StdEMBLseqId" } ,
+ {
+ asn1 "Seq-id.pir" ,
+ label "pir" ,
+ prefix " " ,
+ form
+ use-template "VersionTextseqId" } ,
+ {
+ asn1 "Seq-id.swissprot" ,
+ form
+ use-template "VersionTextseqId" } ,
+ {
+ asn1 "Seq-id.patent" ,
+ form
+ use-template "StdPatentSeqId" } ,
+ {
+ asn1 "Seq-id.other" ,
+ label "REFSEQ:" ,
+ prefix " " ,
+ form
+ use-template "VersionTextseqId" } ,
+ {
+ asn1 "Seq-id.general" ,
+ form
+ null NULL } ,
+ {
+ asn1 "Seq-id.gi" ,
+ label "gi:" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Seq-id.ddbj" ,
+ form
+ use-template "VersionTextseqId" } ,
+ {
+ asn1 "Seq-id.prf" ,
+ form
+ use-template "VersionTextseqId" } ,
+ {
+ asn1 "Seq-id.pdb" ,
+ form
+ use-template "StdPDBseqId" } ,
+ }
+ } } } }
--- /dev/null
+>Alu
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+ggcgggcggatcacctgaggtcaggagttcgagaccagcctggccaacat
+ggtgaaaccccgtctctactaaaaatacaaaaattagccgggcgtggtgg
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+ccagcctgggcgacagagcgagactccgtctcaaaaaaaaaaaaaaaaaa
+>MIR
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+ttrgytattatt
+>L1
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+agaggaacatcacactctggggactgttatggggtggggggcaggggcag
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+agcacaccaacatggcacatgtatacatatataacaaacctgccgttgtg
+cacatgtaccctaaaacttgaagtataataataaaaaaaa
+>THE1
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+cccataattcccacgtgtcgtgggagggacccggtgggaggtaattgaat
+catgggggcgggtctttcccgtgctgttctcgtgatagtgaataagtctc
+acgagatctgatggttttataaaggggagttyccctgcacangctctctt
+gcctgccgccatgtaagacgtgmctttgctcctccttcgccttcygccat
+gattgtgaggcctccccagccatgtggaactgtgagtccattaaacctct
+ttyctttataaattacccagtctcgggtatgtctttattagcagcatgag
+aacggactaataca
+>MLT1
+tgtggtagccagcctccaagatggcccccaatgatccctgctcctggtat
+tcacayccttgtatggtcycytcctacattgaryyagggctrgtctgtgt
+gaccaatagaatagggcagaggtgatgaratrtcacgtgattacgcgtac
+gtgattatgtaasattcagtctttgmcgtcattcttgccgagagactctc
+ctsctggtyttgaagaagtaagctgccacgtcatgagnnnncnnannaga
+rygccgcaaggcaagggnntctagagctgagagtcgcccttactgatggg
+aagtccacgtggsaaggaactgaggtctcctgccaacagccagcttcgac
+ytgccagccatgtgagtgagccatcttggaagcggatcctccagccccag
+tyaagccttcagatgactgcagccccggctgacatcttgactgcaacctc
+atgagagaccctgagccagaactacccagctaagctgctcctarattcct
+gacccacatgtggtaggcwgaataatggctccccaaagatgtccacgtcc
+taatccccagaacctgtgaatatgttaccttacatggcaaaagggacttt
+gcagatgtgattaagttaaggatcttgagatggggagattatcctggatt
+atccgggtgggcccaatgtaatcacaagggtccttawaagagggaggcag
+agggtcagagtcagaagaaggagatgtgacgatggaagcagrragngaaa
+actcaacgttgctggctttgaagatggaggaaggggccatgagccaagga
+atgcgggcagcctctagaagctggaaaaggcaaggaaacggattctcccc
+tagagcctccagaargaacgcggccctgccgacaccttgattttagccca
+gtgagacycattttggacttctgacctccagaactgtaagataataaatt
+tgtgttgttttaagccactaagtttgtggtaatttgttacagcagcmaya
+ggaaactaataca
+>MSTAR
+gaawattggtactgaggagtggagcattgctataaagatacctgaaaatg
+tggaagcgactttggaactgggtaacaggcagaggttggaagagtttgga
+gggctcagaagaagacaggaagatgagggaaagtttggaacttcttagag
+acttgttaaatggttgtgaccaaaatgctgatagtgatatggacagtaag
+ggccaggctgacgaggtctcagatggaaatgaggaacttattgggaactg
+gagcaaaggtcactcttgttatacattagcaaagagcttggctgcatttt
+gcccctgccctagagatttgtggaagtttgaacttgagagtgatgatcta
+gggtatctggcggaagaaatttctaagcagcaaagcgttcaagatgtgac
+ctggctgcttttaacagcttacagtcatatgcgagagcaaagaaatcact
+taaagttggaatttatatttaaaagggaagcagagcgtaaaagtttggaa
+aatttgcagcctggccatgtgatagaaaagaaaaacccgttttctggaga
+gaaattcaagcaggctgcggagcgaccgtttgctaaagagattagcataa
+ctaaaaggaagccaagtgctgatagccaagacaatgggaaaaaggcctcg
+aaggcatttcagaaatcttcgaggtggtccttcccatcacaggcccagag
+gcctaggaggactgaatggtttcgtgggccaggcccagggccccgctgcc
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+gccgtggctcaaagggccccaggtacagctcgagctgccgcttcggagag
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+aggatgtatgggaaatcctgggtgcccaggcagaagcctgctgcagggac
+ggagccctcacagagaacctctactagagcagtgccaaagggaaatgtgg
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+gtgggaagggggccactgtcctccagaccccagaatggtagagccactgg
+cagcgtgcaccgccagcctggaaaagccgcaggcatcagactccaacccg
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+acacggagtcaaaggagattattttggagctttaagatttaatgactgcc
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+atttctcccttttggaatggaaatatttacccaatgcctgtaccaccatt
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+aaggaacttgccttgtctcagatgagactttggactttggacttttgagt
+taatgctggaatgagttaagactttgggggactgttgggaaggcatgatt
+gtattttgcaatgtgagaaggacgtgagatttgggggaaccaggggcaga
+a
+>MLT2B2
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+atagctggttaaacattatttctgggtgtgtctgtgagggtgtttccaga
+tgagattagcatttgaatcagcggactgagtaaagaagattgccctcacc
+aatgtgggcgggcatcatccaatccgttgagggcctgratagaacaaaaa
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+ttctcctgcccttggacattagaactccaggttctcgggccttcggacty
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+tgaryyacgccaccggcttccctggttctccagcttgcagacggcatatc
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+cycytctatccatcctattggttctgtctctctggagaaccctgactaat
+aca
+>LTR1
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+gaagggggaaaggaagtgctgtgtggaggaggatgtggtccctggctagt
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+ccaagaccaccctggcctgccatgcccccatcctgtgcctataaaaaccc
+aagaccctaataaggcagagatagaagcagctggacgtcatgaggaacac
+atcagtggaagagcacacaagcggctagtcatcaagagctcaccagtgga
+agagcagcccgataggcactggcacgcaggcaggtaccggcatgccagca
+ggccatcgactggcaaaatgatgccgaatttggctggagtggtcagagaa
+gagccaggtcactgagctgccggactccaggggaaaaccatctcccttct
+ggctcccccatccactgagagctatttctactcaataaaaccttgcagtc
+attctccaggcccacatgtgatctgattcttctggtacatcaaggcaaga
+aaccccaggatacagaaagccctctgtccttgtgacaaggtagagggtct
+aactgagctggttaacacaagctgcctgtagatggcaaactaaaagagca
+ccttgtaacacatgcccactggagcttcaggagctgtaaacattcacccc
+tagacactgccatgggattggagccccacagcttgcctgtccaaatgctc
+ccctagaggtttgagcagcagggcactgaagaagtgagccacacccccat
+cacatcccctgtgaggggaacaagggaacctttcctatttca
+>LTR2
+taaggaaggagaccacctctcccattgtctcctgtttcatgagaaagcaa
+aaagttaaaaaaagaagcagaagtgagatcaatggccagatggtttagtg
+ccaagaaccaggcctggtagttaaacatcaactcctgacctaaccgcttg
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+tagcccccacttgcacaatgtatcatgaccctttcacgtggacccctcag
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+tcttgagacgcgagtctaccaatgctcccagctgattaaagcctcttcct
+tcatagaaccggtgtctaagaggttttgtctgtgactgttcctgctaca
+>LTR3
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+gctatatgagcaaacagcaaactgttctcatgaatgcaggatgctggcaa
+gctgacaactgcatctgccaccagaaggaatgctgagggcagtcataccc
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+>LTR4
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+cctgaccagtctgactcactccaaagtcctgctggagctatgataattat
+ctgcaaggccaggcaggggctccgaaggagggctccaggagcagggatga
+gaaaaacaagttctccttatcagtttccctgtttgaaattctctccccat
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+aagtctgtaaagattttgtaagttcttgtttttctttctgtagcatggca
+aggtcacaagacatgtttaagtaaggtaggctcatgttgcaaatcctgtt
+gtaaaacctgtcacggtatgattaactgcctttgttctgcttctgtaaga
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+ctgatgcatgtataaaagtcaagcccgtctttgttccgggctcagccttt
+ggatgttaatccgctgggccagtggccacctaaataaaaccttcctgttg
+cacccagtgatctctccggcctcctgatacccacaaca
+>LTR5
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+aagtagacataggagactccattttgttctgtactaagaaaaattattct
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+gaaacatgtgctgtgtcaaactcagggttaaatggattaagggcggtgca
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+ccatgtgagagtctgaaatatggcctcgtgggaagggaaagacctgaccg
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+tccccgggcccccttatttctttctctatactttgtctctgtgtcttttt
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+>LTR6
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+gtgcctaagtcgagtgaagcctttagattaattctttttatttatctctc
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+aatgccctgccccaccttaactgatgacattccaccacaaaagaagtgaa
+aatggccggtccttgccttaagtgatgacattaccttgtaagagtccttt
+tcctggctcatcctagctcaaaaatctcccctactgagcaccctgcgacc
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+tacctacccaaatcctataaaacagccccacccctatctccctttgctga
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+>LTR8
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+taactgcttttatcttgcttttaacctttaagctgtccttgtttattcct
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+ttaaacaaagacagtaacagccctttcccaagcagacctccttcatgcct
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+aaactgctcctaagatcagtgcttgagatattttgcagaccctgcccttg
+acggatcagctggcaccaaccagatcaatcaactggctcatctgatcttg
+cggcccccacccaggaactgactcagcgcaaaaagacagcttcaacttcc
+tatgatttcatccctgaccaatcaacactcctggctcactggcttccccc
+cacccaccaagttatccttaaaaactctgattcctgaatgctcagggaga
+ctgattggagtaacaataaaactccagtctcccacacagacggctctgtg
+tgaattactctttctccattgcaattcccctgtcttgttgaatcggctct
+gtccaggtagtgtgcaaggtgaaccccttgggtggttaca
+>LTR9
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+agcaagggtatgggagtcctcagtaaggcttttatttttaatgaaaagca
+gccccaaatcattttctaacaaaaagcaccctgcaagctggaagtttgca
+caggtggatgctggcaggaactaaggattagatatgttcaagatggtggt
+tccatcttcccttctttgccagccaggtgtactgtaaaggagcagacaag
+atggcgctaatcaactggaaagcccagttgcataaaaagattaggcttcc
+ctgcgcaccatgcaaacgtcatatctgatcaaaccaatctatgagctcta
+tgtaaatcagacaccacttcctcaaactggactataaaactcgatggatt
+caccaccagctggtcttttccgcttggagaccccttcctctatagaggaa
+gctgtttctctttgtcttctctcctacccattaaacctctgctcctaaac
+tcctcatgtgtgtccatatcctaaattttcctggcacgtgacaacaaacc
+ccagtgtatacacaccccagacaacatagccacttcaaaatgggggctcg
+tctgggat
+>LTR10
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+ctagggttggactgcacagtctaagctaattccgattggctactttaaag
+agagcaggggtatgagccagagtggcggggtgagtagtttggtgggaagg
+gtggtt
+>LTR11
+tgtgtttctgcaggatgtacagccctcccagcacggtgctcgcttcccta
+atgccattccacagtatttgttgcagagaaggaaggcagcatgccaggac
+agatggagacaggactaatttggcctgaggtatgtaattttgaacttgag
+cctctctctgggactgtaaaactccaaatcaaagctaatctgagaataca
+tacatctgaaagatgattaggactgtaaacatctattaatattcaactct
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+agaaaaaaaaaaaagcacacagcatatgcactggaaagtttcgcttattc
+aaaacagtatttgtcaagcacctccagtctggtgctgcaggggaaacaaa
+gattaaacagccaggcggacactgctctgcttccaaggtgcttacggtct
+taagaaggagacaagacatgtttataaatagccaaaatgcaacccagaaa
+aggctaaaaaacactgagagggagggagaaataaacgaagcaagaggtct
+ccggaggaagagatgaatgaattagcctattaataactccgtcactgtaa
+tcccaatgtaaagcaagaattccaaaccaggaaaggtcaaactgaagtat
+ttgaggaacacaggcgtcgcctaagcccttcaca
+>LTR12
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+gggattgtaaatacaccaatcagcactctgtatctagctcaaggtttgta
+aacacaccaatcagaaccctgtgtctagctcagggtttgtgaatgcacca
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+gtctagctaagggattgtgaatgcaccaatcggcactctgtatctagctc
+aaggttgtaaatggaccaatcagcactctatgtctagctcagtgtttgta
+aatacaccaatcgacactctatctagctaatctagtggggacgtggagaa
+cttttgtgtctaactcagggatgtaaatgcaccaatcagaaccctgtcaa
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+caatcagcaggatgtgggtggggccagataagagaagaaaagcaggctgc
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+tttgttctttcgctctttgcaataaatcttgctgctgctcactctttggg
+tccacactgcctttatgagctgtaacactcaccgcgaaggtctgcagctt
+catctgaagcagcgagacacgaacccaccaggaggaacaaacaactccga
+tgcgctgccttaagagctgtaacaccgcgaggtctcgagcttcactcctg
+agccagcaagaccacaaacccaccagaaggaagaaactcaggaaaacagc
+cgaacatcagaaggaataaactctggacacaccacctttaagaactgtga
+cactcgctgcgagcgtctgtggcttca
+>LTR13
+tgtgggccgcaagccagggagctgcccaggcaagagcctgaaggcacaag
+ctgttccagtacagcaaagaaaataattagaataagaaaagttttactag
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+agggccgctggagggctccttggcctagcggtaatgccagtgcctgggaa
+ggccctggttacttagcaggccttggtctagcggtggccccagtgcctgg
+gaaggcacccgttacttagcagacccggaaaggaatctccctctctccag
+gggagacagagaacgctccgctccaccacctcttgtgggaggtctgacat
+tagccaggccgggccgagtcatccggaggctccaacgtctgtctccctgt
+gatgctgtgcttcagtggtcacgctccttgttcactttcatgttcagcct
+gtgcacctggctcctccttttaagttcttagaagacagcagtagcagaac
+tagtaggagtaccacagtcttcgatctttctgataagtgcatagaagaaa
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+ggccccctgtccagtggacacgtgactcgcgtgacctatcgatcattgga
+gatgactggcactccttaccctgcccccttgccttgactacaataaatag
+cagcgcctccaggcactcggggccactacctgtctgtctccgcgctttgg
+tggcagtggtcccccgggcccagctgtctttcttcctatctctttgtctt
+ctgtctttatctcttcgatctctcgtctccgcacacacgcgaagagaaaa
+cccacagacccggtaggggtggaccctaca
+>MER1
+caggggtccccaacccccgggccacggaccggtaccggtccgtggcctgt
+taggaaccgggctgcacagcaggaggtgagcggcgggcgagtgagcgaag
+cttcatctgtakttacagccgctccccatcactcgcattaccgcctgagc
+tccacctcctgtcagatcagcggtggcactagattctcataggagcgcga
+accctattgtgaactgcgcatgcgagggatctaggttgcgcgctccttat
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+ttatggtgagttgtrtaattatttcattatatattacaatgtaataataa
+tagaaataaagtgcacaataaatgtaatgcacttgaatcatcccgaaacc
+atcccccccccctggtccgtggaaaaattgtcttccacgaaaccggtccc
+tggtgccaaaaaggttggggaccactg
+>MER2
+cagtcgyccctccgtatccgtgygttccacatccgtggattcaaccaacc
+gcggatcgaaaatattcaggyaaaaaattgyatggttgcgtctgtactga
+acatgtacagacttttttncttgtcattattccctaaacaatacagtata
+acaactatttacatagcatttacattgtattaggtattataagtaatcta
+gagatgatttaaagtatacgggaggatgtgcgtaggttatatgcaaatac
+tacgccattttatatcagggacttgagcatccgcggattttggtatctgc
+ggggggtcctggaaccaatcccccacggataccgagggatyactg
+>MER3
+cagcgctgtccaatagaactttctgtggtgatggaaatgttctatatctg
+cgctgtccaatacggtagccactagccacatgtggctaytgagcacttga
+aatgtggytagtgcgactgaggaactgaatttttaattttatttaatttt
+aattaatttaaatttaaatagccacatgtggctagtggctaccatattgg
+acagcgcag
+>MER4
+gttrgngttrgngattgcnnntgtgaaaggaaaataaatctcgggrcccc
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+acctgcctcccattttattcctaaataagatagctacaaagataaaaggc
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+gagacctgtctcagatacttttgggttcaca
+>MER5
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+ggaacttgttagaaatgcagattctcgggccccaccccagacctactgaa
+tcagaaactctgggrgtggggcccagcaatctgtgttttaacaagcyctc
+caggtgattctgatgcatgctcaagtttgagaaccactg
+>MER6
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+gytgatgagraaaaaaatcgattcccggccggggccactgtctgtgtgga
+gtttgcacgttctccccatgtctgcgtgggttttctccaggtactccggt
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+cgggataggctctggccacccgtgaccctgaamtggaataagtgnrttgr
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+gtgatcagtgagcctgccatatatgttattgcttgtttctgaactgagtg
+gtgggaggaggtgttcctaacaatgttcactttgcagacatttatttctt
+tatttaatccattatcactatgaccactgtcattcagtkattcwccaaaa
+attgggtaaataattatcwtryttgtttttattaatctttcttaaatgta
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+tttatttagaagtttggtgatgtttttgtgaccagaaatatgccatagga
+acttaactcttgtttatatcaattagcctrtggtaaaattggtttcgtta
+tacgtcgtttcacttaaagtcgcagtttccaagaacctatcaacgacgtt
+aagtgaggacttactg
+>MER7
+cagtcatgcgtcgcttaacgacggggatacgttctgagaaatgcgtcatt
+aggcaatttcgttgtgcgaacatcatagagtgtacttacacaaacctaga
+tggtatagcctactacacacctaggctatrtggtatagcctattgctcct
+aggctacaaacctgtacagcatgttactgtactgaatactgtaggcaatt
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+tcatctcctatgataacgatgcyttcttctggaatatctcctgaaggacc
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+ccgtcgtatatgtggtccatcgttgaccgaaacgtcgttatgcagcgcat
+gactg
+>MER8
+cagttgtccctctgtatanncgggggattggttccaggacccytgtgtat
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+>MER9
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+>MER11A
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+t
+>MER20
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+>MER21
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+>MER22
+gagctctgggcttccatacctgtgtgggacagggaagctctctcggtctc
+catggcccaagtgatggctgcacgctcggtccaggaagaggcggaggaag
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+>MER25
+acaaantagggaaaaatggcggataggaggcaggactaaattgcagctcc
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+>MER31
+caccctgcgtatctgaycaggttcctcartctccgccgtcccccaggtaa
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+gcagaatctccttactcctgatgtttcctcttrgtaattttccatccact
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+>MER33
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+>MER34
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+>MER35
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+>MER39
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+>MER41
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+>MER42
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+tttgaaattacttcaaaataaa
+>MER43
+cccaagcccagtaacgctgtggctcttgcagactcntagaggtactgcct
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+actcttgttctcttcccttactttctcccaaacaaacaaatggagtctct
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+>MER44C
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+>MER45
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+>MER46
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+>ALR
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+>MSR1
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+>TAR1
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+gtctctgcgccgccggggacgtgtgtctctgcgcgtgcaccgcgccaccc
+ccgcgctccccgcccggcggcgcgcgactgtgcgactgcaacactccccg
+ccaccctcagcccagcgacgtgcgtctctgcgcctgcgccgcgcctcact
+cccgcccgctcagcgacccctcccttccggggaggcgccggcgtgcgtct
+acgccctgcgccgcgtctccccaacagcggcgcgcctctctgcgcctgcg
+ccggcgcgccgcgcctctctgcgcctgcgccggcgcgccgcgcctctctg
+cgcctgcgccggcgccccgcgcctctctgcgcctgcgccggcgccccgcg
+cctctctgcgcctgcgccggcgccccgcgcctctctgcgcctgcgccggc
+gccccgcgcctctctgcgcctgcgccggcgccccgcgcctctctgcgcct
+gcgccggcgccccgcgcctctctgcgcctgcgccggcgccccgcgcctct
+ctgcgcctgcgccggcgccccgcgcctctctgcgcctgcgccggcgcccc
+gcgcctctctgcgcctgcgccggcgccccgcgcctctctgcgcctgcgcc
+ggcgccccgcgcctctctgcgcctgcgccggcgccccgcgcctctctgcg
+cctgcgccggcgccccgcgcctctctgcgcctgcgccggcgccccgcgcc
+tctctgcgcctgcgccggcgccccgcgcctctctgcgcctgcgccggcgc
+gccgcctttgcgagggcggagttgcgttctctttagcacacacccggaga
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+tgcctgcctttgggataactcggggccgcatcgagggtgaataaaatctt
+tcccgtttgctgccctgaataatcaaggtcagagaccagttagaacggtt
+tagtgtggaaagcgggaaacgaaaagcctctctgaatcctgcgcaccgag
+attctcccaaggcaaggcgaggggctgtattgcagggttcaagtgcagcg
+tcagaactcaaatgcagcattcctaatgcacacatgacaccctaaatata
+acaggcatattactcatggagggttagggttcaggttcgggttcgggttc
+gggttcgggtt
+>CER
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+acaactgccatggtctgaatggttgtccctcacatagtattccagaacac
+tgctatgagggtctgaatgtttgtacctcacataggattccagaacactg
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+tggggtctgaatgtctgtccctcacatcggattccagaaccctgctgctg
+gggtttgaatgtctgtccctcacatagaattc
+>BSR
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+ttctattcg
+>HSATI
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+gtgtaanngcactcntgtcyycctggcagcagttggacctcgcgatgtgg
+attgtgccctcacccagcnntntttatgccctntcnccatggtgacngga
+ttaggggtctcctgctcttcnntcctaaggaccactgtctgtgctgtgtc
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+ttgctttttctcnntggggaacctgtgttgctgctttgaaggtatattca
+tactggccnntcanntgnncaacatcnncaaantnactagttanggcttt
+caaaatatgntatttcaaaaaattanccgtctgtattttccatatgcagt
+tataagtaggtttcatcggttatgttttattcctcagtttatacatttga
+ttattgtaccaagcagagtacctttgaaattttttttcatttaaaaaata
+tggatctttaaaaaaaaattatatatgatatatattacatgttatgtgct
+atgccttatntgtaacatataacctcatatattttntatgtcatagtata
+taatatttatcctgtgtcatcttatatatac
+>SAR
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+>SN5
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+tccaaggcccaggagcccagcttctgggcctccaagccaggccatctggc
+gagggagtcggtggacgtgccctggcttcttccatgttgagttggtacta
+cccaccaaggggggtagagaggcgagcagatgttgtctctggcctgtgtc
+ttgttatcatggtgctgactaggcctggtacagggccctgatggggttgt
+cctgggtggtcacgggggtgatgagaagaagatgcagaatggattgctgt
+gaggatgaatgagacgactgtcagtacagacaggcacacggtgaagtgtt
+cagggattcccctcagtagctgcccagacccaaaacctgactcctgagtc
+acgttactgtcccactatacgttaagaggagggaaagctgggtcgcgcag
+gtccc
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+ggttgtgatcaattagttgtaaacancgctgcactccaaccagcc
+>HIR
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+agtgtccataaatcactcagggagggcccccatggatacagggccgtagt
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+taggaccatattataattttcgggttcccaggtgcacgtttccaataacc
+aggtgcacggatgtatagggtcccccccatggatagaggtccgtgttagg
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+accatgttttaatttttca
+>7SK
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+tgattcggctgatctggctggctaggcgggtctcctcttcctccctcagc
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+cgagtagctgtgctcccctgctagaacctccaaacaagctctc
+>KER
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+aggtgaggangnccctatgcattcagatgtggcccaccctggggtctggt
+ggactaaagncttggacaccccagatcagccttagtgggatgaggcagga
+aagacagctgagggtcagaacccaggcaggtccaatgccagggtgggcat
+ttcgagttggtgagacatttcaccctggtgccaagct
+>XTR
+ttaatttgagagaaattaattattctgcaacttagggacaagtcatgtct
+ttgaatattctgtagtttgaggagaatatttgttatatttgcaaaataaa
+a
+>XBR
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+tcaagttaatatgttttccttcattgtatagtatgtaactacggacacta
+ttagaggagggatttgtgtagcacttaggacattatacttgataatttcc
+aagggtctttctagatttaaaagtctgattctaacgtagtaataaaaata
+aaggcccaattttctctttaatattgcctgaagatattactctattattg
+cattaaaattaaacattcacacattgtttgcactgctaaataaaattatg
+taa
+>Mariner1
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+tttgatattggaatacattcttaaataaatgtggttatgttatacatcat
+tttaatgggcatttctcgctttacgtttttttgctaatgacttattactt
+gctgtttatttkrtgtttattttagactatgnaaatgatgttagacaaaa
+agcarattcgagcgattttcttattcaagktcaaamtgrrtcgtaaagcg
+gcggagacaactcgcaacatcagcaacgcatttggcccaggaactgctaa
+taaacatacagtgcagtggtggttcaagaagttttncaaaggagacgaga
+gccttgaagatgaggagtgtaatgacgggccatcagaagttgacaacgac
+cagttgagagcaatcatcgaarycgatcctcttacaactanacgagaagt
+tgctgaagaactcgacgttgaccattctacggtcgttcggcatttgaagc
+aaattggraagnaaaaactcgataagtgggtgcctcataaagtgagcaaa
+actttttnaaattgtcattttaaagtgtcatctcttattctatgcaataa
+caacgaaccatttcttgatcagattgtgacgtagaacgaaaagtggattt
+tatacgacaaccggcgacgaccagctcagtggttggaccgaaagaagctc
+caaagcacttcccaaagccaaacttgcaccaaaaaagtcgcggtcgcggt
+ctggtggtctgctgccagtgtgatccaccacagctttctgaatcctggca
+aaaccattacatctgagaagtatcttcagcaaattgatgagatgcaccaa
+aaactgcaatgcctgcacctggcattggtcaacagaaagggcccaattct
+tctccacgacaacgcccgaccgcacgtygcacaaccaacgcttcaaaagt
+tgaataaattgggctacgaacttttgcctcatccgccatattcacctgac
+ctctcgccaacaaactaccacttcttcaagcatctcgtcaactttttgca
+gggaaaacgcttccacaaccagcaggatgcagaaaatgctttccaagagt
+tcgtcgaatcccaaagcacggatttttatgctacaggaataaacaaactt
+atttctcgttggcaaaaatgtgttgattgtaatggttcctattttgatta
+ataaagatgtgyttgagcctagttatgattatgatttaatggccaaaacc
+acaattacttttgcaccaacctaa
+>Tigger1
+caggcatacctcgttttattgcgcttcgctttattgcgcttcgcagatac
+tgcgttttttacaaattgaaggtttgtggcaaccctgcgttgagcaagtc
+tgtcggcgccatttttccaacagcatgtgctcacttcgtgtctctgtgtc
+acattttggtaattctcgcaatatttcaaactttttcattattattatat
+ctgttatggtgatctgtgatcagtgatctttgatgttactattgtaattg
+ttttggggtgccacgaaccgcacccatataagacggcgaacttaatcgat
+aaatgttgtgtgtgttctgactgctccaccgaccggccgttcccccgtct
+ctctccctctcytcgggcctccctattccctgagacacaacaatattgaa
+attaggccaattaataaccctacaatggcctctaagtgttcaagtgaaag
+gaagagtmrcacatctctcactttaaatcaaaagctagaaatgattaagc
+ttagtgaggaaggcatgtcaaaagccgagataggccaaaagctaggcctc
+ttgcgccaaacagttagccaagttgtgaatgcaaaggaaaagttcttgaa
+ggaaattaaaagtgctactccagtgaacacacgaatgataagaaagyaaa
+acagccttattgctgatatggagaaagttttagtggtctggatagaagat
+caaaccagccacaayattcccttaagccaaagcctaatccagagcaaggc
+cctaactctcttcaattctatgaaggctgagagaggtgaggaagctgcag
+aagaaaagtttgaagctagcagaggttggttcatgaggtttaaggaaaga
+agccatctccataacataaaagtgcaaggtgaagcagcaagtgctgatgt
+agaagctgcagcaagttatccagaagatctagctaagatcaytgatgaag
+gtggctacactaaacaacagattttcartgtagatgaaacagccttctat
+tggaagaagatgccatctaggactttcatagctagagaggagaagtcaat
+gcctggcttcaaagcttcaaaggacaggctgactctcttgttaggggcta
+atgcagctggtgactttaagttgaagccaatgctcatttaccattctgaa
+aatcctagagcccttaagaattatgctaaatctactctgcctgtgctcta
+taaatggaacaacaaagcctggatgacagcacatctgtttacagcatggt
+ttactgaatattttaagcccactgttgagacctactgctcagaaaaaaag
+attcctttcaaaatattactgctcattgacaacgcacctggtcacccaag
+agctctgatggagatgtacaaggagattaatgttgttttcatgcctgcta
+acacaacatccattctgcagcccatggatcaaggagtaatttcgactttc
+aagtcttattatttaagaaatacattttataaggctatagctgccataga
+tagtgattcctctgatggatctgggcaaagtaaattgaaaaccttctgga
+aaggattcaccattctagatgccattaagaacattcgtgattcatgggag
+gaggtcaaaatatcaacattaacaggagtttggaagaagttgattccaac
+cctcatggatgactttgaggggttyaagacttcagtggaggaagtaactg
+cagatgtggtggaaatagcaagagaactagaattagaagtggagcctgaa
+gatgtgactgaattgctgcaatctcatgataaaacttgaacggatgagga
+gttgcttcttatggatgagcaaagaaagtggtttcttgagatggaatcta
+ctcctggtgaagatgctgtgaacattgttgaaatgacaacaaaggattta
+gaatattacataaacttagttgataaagcagcggcagggtttgagaggat
+tgactccaattttgaaagaagttctactgtgggtaaaatgctgtcaaaca
+gcatcacatgctacagagaaatctttcatgaaaggaagagtcaattgatg
+cggcaaacttcattgttgtcttattttaagaaattgccacagccacccca
+accttcagcaaccaccaccctgatcagtcagcagccatcaacatcaaggc
+aagaccctccaccagcaaaaagattacgactcgctgaaggctcagatgat
+cgttagcattttttagcaataaagtatttttaaattaaggtatgtacatt
+gttttttagacataatgctattgcacacttaatagactacagtatagcgt
+aaacataacttttatatgcactgggaaaccaaaaaattcgtgtgactcgc
+tttattgcgatattcgctttattgcggtggtctggaaccgaacccgcaat
+atctccgaggtatgcctg
+>Tigger2
+cagttgacccttgaacaacacgggtttgaactgcgcgggtccacttatac
+gtgrattttttycaataaatatattggaaaaawttytggagatttgcaac
+aatttgaaaaaactcgcagacgaaccgcgtagcctagaaatattgaaaaa
+attaagaaaaaggtatgtcatgaatgtataaaatatatgtagatactagt
+ctattttatcatttactaccataaaatayacacaaanctattataaaaag
+ttaaaatttatcaaaacttayayayayacttacagactgtacgtggtacc
+attcgaagtngagagaaatataaacaaacntaaagatgcagtattaaatc
+acaactgcgtaaaattaactgtagtacatactatactaccgtaataattt
+tgtagccacctcctgttgctattgcagcgagctcaagtgttgtgagtacc
+tgcttaaaacgctskgtgatgctaatcatctccgcgcgagcagttyatct
+ctccagtaaattgcgtattgcagtaaaaagtgatctctcacggttctcgc
+gtatttttcattgtgtttartgcaatattgtaaaccttgaataacaccat
+gggacccatacgaagtgccactagtgatgctggaagtgctcccaagaagc
+agagaaaagtcatgacattacaagaaaaagttgaattgcttgatatgtac
+catagattgaggtctgcagctggggttgcctgccatttcaagayagatga
+atccggcgtaaggaccgttgtmaaaaaagaaaaggaaattcgtgaaracc
+gtcgctgcagttatgcccagcaggcacaaaaacttgtnactttttgcgaa
+atacctttttatgttgtattgaaaatgcagcttttntgtgggtgcaggat
+tgctataagaaaggmatacctanagactctaatatgattagagaaaaagc
+gaagtcattatgtgannacttaaagcaaaarraagatgamrgatctaaag
+ctgganaatttaatgccagcaaakgatggtttgacaattttagaaagarg
+twtggcttaaaaaatktcaagakaacaggagaagcasyttctgctgacca
+agagacagcagacgagttnccagatgccattaacaaaatcattgaggaga
+aaggatatctgcctgaacaggtttttaatgcagatgaragtgccctattc
+tggggggaaaaaatgccacaaagracatttattagtaagnaagagaagcg
+agcaccaggatttaaggcargaagggataggctaactctactgttttgtg
+caaatgcagttaggtttatgatcaggactgcccttatctataaagctgct
+aacccccgagccttgaagggaaaagataaacgccagctgccagtcttttg
+gttgtacaacaagaaggcctggacaacgagaaccctttttctggattggt
+tccattkatgctttgtccctgawgtcaggaagtaccttgccagtaagrga
+ctgccttttaaagttcttttgatattggacaatgcccytggccacccaga
+accccatgagttcaacaccgaaggtgtcgaagtggtctacttgcccccaa
+acacaacgtctctaattcagcctctagatcagggggtcataaggaccttt
+aaggctcattacacacggtactctatggaaaggattgtcaacgctatgga
+agagaaccccgatagaragaacatcatgaaagtctggaaggattacacca
+ttgaagatgccattgttrttatagaaaaagccgtgaaagccatcaagccc
+aaaacagtaaattcctgctggagaaaactgtgtccagatgttgtacatga
+cttcacaggatttacgacagagccaatcaaggaaatcatgaaagagattg
+tggatatggcaaaaaagttggggggtaaagggtttcaagatgcgaatctt
+ggagaaattcaagagcwaatagacaccacaccagaggaattaacagaaga
+cgacttgatggagatgagtgcttccgaaccagtgccagacgatgaggaag
+aagacatngaagaagcagtgccagaaaacaaattgacattagacaatctr
+ggcagaagggttccaattattcaagactgcttttgacttcttttacaaca
+tggacccttctatgatacgggcactgaaactaaagcaaacagtggaagaa
+ggattggtaytatacagaaacatttttagagaaatgaaaaggcaaaaayr
+tcagacagaaattacgatgtatttccgtaaagttacaccgagtgtgcctg
+cctctcctgcctccccttccacctcctccacctcttccacctctgccacc
+ctgagacagcaagaccaacccctcctcctcctcagcctwctcaatgtgaa
+gacgacgaggatgaagacctttatgatgatccacttccacttaatgaata
+gtaaatatattttctcttccttatgattttcttaataacattttcttttc
+tctagcttactttattgtaagaatacggtatataatacatataacataca
+aaatatgtgttaatcgactgtttatgttatcggtaaggcttccagtcaac
+agtaggctattagtagttaagttttkggggagtcaaaagttatacgtgga
+tttttnactgcgcggggggtcagcgcccctaacccccgcgttgttcaagg
+gtcaactg
+>PAB
+ccttaccagccccctactgtggcaggccaggtcccactaacacaggcctc
+cataacaactgtttcagctctgactgagtggttaagttaaatactaaaag
+ccgagagagccagtccccttatacagaggctggaatgtaacaaaagccca
+ccaagagttttgcctaggcctttcctgggccttgaagcatgacaaaataa
+caaaagaattcttaacagaatctatttaggattaaacaagttttactggg
+ggttctgaagaaactccccagtcctccacaaacaagtttactggggtctg
+aaagaactccccaaacctccatgatttagcaggagacaagataagggtaa
+tcaccccagcacctggacccagctagatttagtcaatttactgaggctac
+aaaggaaggtcttcaggactcagacctcagttatagattagaagaagtta
+atcacttatgtctttagatgattgcacacttacacatagacatatagctt
+agaaggtgtataagctctggaaaactttgtaattttgagttggtctggtg
+atattttccaggccttctccctatacccggttacagaaataaaaactttc
+ttcctccccagttcatctgcatcttgttaatgggctgccagaaatagcag
+cccaaccctcagttaggtctgggaacactaccccccaacacacacacaca
+cac
+
--- /dev/null
+13
+9 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Buchnera
+34 Bacteria; Proteobacteria; Deltaproteobacteria; Myxococcales; Cystobacterineae; Myxococcaceae; Myxococcus
+139 Bacteria; Spirochaetes; Spirochaetales; Spirochaetaceae; Borrelia; Borrelia burgdorferi group
+160 Bacteria; Spirochaetes; Spirochaetales; Spirochaetaceae; Treponema
+173 Bacteria; Spirochaetes; Spirochaetales; Leptospiraceae; Leptospira
+188 Bacteria; Proteobacteria; Alphaproteobacteria; Rhodospirillales; Rhodospirillaceae; Magnetospirillum
+197 Bacteria; Proteobacteria; Epsilonproteobacteria; Campylobacterales; Campylobacteraceae; Campylobacter
+210 Bacteria; Proteobacteria; Epsilonproteobacteria; Campylobacterales; Helicobacteraceae; Helicobacter
+263 Bacteria; Proteobacteria; Gammaproteobacteria; Thiotrichales; Francisellaceae; Francisella
+274 Bacteria; Deinococcus-Thermus; Deinococci; Thermales; Thermaceae; Thermus
+287 Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Pseudomonas
+292 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Burkholderia; Burkholderia cepacia complex
+294 Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Pseudomonas
+303 Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Pseudomonas
+305 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Ralstonia
+316 Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Pseudomonas
+317 Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Pseudomonas
+339 Bacteria; Proteobacteria; Gammaproteobacteria; Xanthomonadales; Xanthomonadaceae; Xanthomonas
+354 Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Azotobacter
+358 Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium
+375 Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Bradyrhizobiaceae; Bradyrhizobium
+382 Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Rhizobiaceae; Sinorhizobium/Ensifer group; Sinorhizobium
+384 Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Rhizobiaceae; Rhizobium/Agrobacterium group; Rhizobium
+394 Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Rhizobiaceae; Rhizobium/Agrobacterium group; Rhizobium
+446 Bacteria; Proteobacteria; Gammaproteobacteria; Legionellales; Legionellaceae; Legionella
+480 Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; Moraxellaceae; Moraxella
+485 Bacteria; Proteobacteria; Betaproteobacteria; Neisseriales; Neisseriaceae; Neisseria
+487 Bacteria; Proteobacteria; Betaproteobacteria; Neisseriales; Neisseriaceae; Neisseria
+518 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Alcaligenaceae; Bordetella
+520 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Alcaligenaceae; Bordetella
+529 Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Brucellaceae; Ochrobactrum
+549 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Pantoea
+550 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Enterobacter
+552 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Erwinia
+554 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Pectobacterium
+562 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Escherichia
+571 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Klebsiella
+573 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Klebsiella
+602 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Salmonella
+615 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Serratia
+623 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Shigella
+630 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Yersinia
+632 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Yersinia
+644 Bacteria; Proteobacteria; Gammaproteobacteria; Aeromonadales; Aeromonadaceae; Aeromonas
+666 Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae; Vibrio
+670 Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae; Vibrio
+672 Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae; Vibrio
+714 Bacteria; Proteobacteria; Gammaproteobacteria; Pasteurellales; Pasteurellaceae; Actinobacillus
+715 Bacteria; Proteobacteria; Gammaproteobacteria; Pasteurellales; Pasteurellaceae; Actinobacillus
+727 Bacteria; Proteobacteria; Gammaproteobacteria; Pasteurellales; Pasteurellaceae; Haemophilus
+731 Bacteria; Proteobacteria; Gammaproteobacteria; Pasteurellales; Pasteurellaceae; Histophilus
+747 Bacteria; Proteobacteria; Gammaproteobacteria; Pasteurellales; Pasteurellaceae; Pasteurella
+770 Bacteria; Proteobacteria; Alphaproteobacteria; Rickettsiales; Anaplasmataceae; Anaplasma
+782 Bacteria; Proteobacteria; Alphaproteobacteria; Rickettsiales; Rickettsiaceae; Rickettsieae; Rickettsia; typhus group
+813 Bacteria; Chlamydiae; Chlamydiales; Chlamydiaceae; Chlamydia
+817 Bacteria; Bacteroidetes; Bacteroides (class); Bacteroidales; Bacteroidaceae; Bacteroides
+837 Bacteria; Bacteroidetes; Bacteroides (class); Bacteroidales; Porphyromonadaceae; Porphyromonas
+851 Bacteria; Fusobacteria; Fusobacterales; Fusobacteriaceae; Fusobacterium
+876 Bacteria; Proteobacteria; Deltaproteobacteria; Desulfovibrionales; Desulfovibrionaceae; Desulfovibrio
+920 Bacteria; Proteobacteria; Gammaproteobacteria; Acidithiobacillales; Acidithiobacillaceae; Acidithiobacillus
+948 Bacteria; Proteobacteria; Alphaproteobacteria; Rickettsiales; Anaplasmataceae; Anaplasma; phagocytophilum group
+1063 Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales; Rhodobacteraceae; Rhodobacter
+1085 Bacteria; Proteobacteria; Alphaproteobacteria; Rhodospirillales; Rhodospirillaceae; Rhodospirillum
+1097 Bacteria; Chlorobi; Chlorobia; Chlorobiales; Chlorobiaceae; Chlorobium
+1108 Bacteria; Chloroflexi; Chloroflexales; Chloroflexaceae; Chloroflexus
+1126 Bacteria; Cyanobacteria; Chroococcales; Microcystis
+1206 Bacteria; Cyanobacteria; Oscillatoriales; Trichodesmium
+1245 Bacteria; Firmicutes; Lactobacillales; Leuconostoc
+1247 Bacteria; Firmicutes; Lactobacillales; Oenococcus
+1265 Bacteria; Firmicutes; Clostridia; Clostridiales; Lachnospiraceae; Ruminococcus
+1280 Bacteria; Firmicutes; Bacillales; Staphylococcus
+1282 Bacteria; Firmicutes; Bacillales; Staphylococcus
+1299 Bacteria; Deinococcus-Thermus; Deinococci; Deinococcales; Deinococcaceae; Deinococcus
+1303 Bacteria; Firmicutes; Lactobacillales; Streptococcaceae; Streptococcus
+1307 Bacteria; Firmicutes; Lactobacillales; Streptococcaceae; Streptococcus
+1308 Bacteria; Firmicutes; Lactobacillales; Streptococcaceae; Streptococcus
+1309 Bacteria; Firmicutes; Lactobacillales; Streptococcaceae; Streptococcus
+1311 Bacteria; Firmicutes; Lactobacillales; Streptococcaceae; Streptococcus
+1313 Bacteria; Firmicutes; Lactobacillales; Streptococcaceae; Streptococcus
+1314 Bacteria; Firmicutes; Lactobacillales; Streptococcaceae; Streptococcus
+1334 Bacteria; Firmicutes; Lactobacillales; Streptococcaceae; Streptococcus
+1336 Bacteria; Firmicutes; Lactobacillales; Streptococcaceae; Streptococcus
+1351 Bacteria; Firmicutes; Lactobacillales; Enterococcaceae; Enterococcus
+1352 Bacteria; Firmicutes; Lactobacillales; Enterococcaceae; Enterococcus
+1358 Bacteria; Firmicutes; Lactobacillales; Streptococcaceae; Lactococcus
+1392 Bacteria; Firmicutes; Bacillales; Bacillaceae; Bacillus; Bacillus cereus group
+1396 Bacteria; Firmicutes; Bacillales; Bacillaceae; Bacillus; Bacillus cereus group
+1402 Bacteria; Firmicutes; Bacillales; Bacillaceae; Bacillus
+1422 Bacteria; Firmicutes; Bacillales; Bacillaceae; Geobacillus
+1423 Bacteria; Firmicutes; Bacillales; Bacillaceae; Bacillus
+1428 Bacteria; Firmicutes; Bacillales; Bacillaceae; Bacillus; Bacillus cereus group
+1488 Bacteria; Firmicutes; Clostridia; Clostridiales; Clostridiaceae; Clostridium
+1496 Bacteria; Firmicutes; Clostridia; Clostridiales; Clostridiaceae; Clostridium
+1502 Bacteria; Firmicutes; Clostridia; Clostridiales; Clostridiaceae; Clostridium
+1515 Bacteria; Firmicutes; Clostridia; Clostridiales; Clostridiaceae; Clostridium
+1575 Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Micrococcineae; Microbacteriaceae; Leifsonia
+1580 Bacteria; Firmicutes; Lactobacillales; Lactobacillaceae; Lactobacillus
+1584 Bacteria; Firmicutes; Lactobacillales; Lactobacillaceae; Lactobacillus
+1590 Bacteria; Firmicutes; Lactobacillales; Lactobacillaceae; Lactobacillus
+1639 Bacteria; Firmicutes; Bacillales; Listeriaceae; Listeria
+1642 Bacteria; Firmicutes; Bacillales; Listeriaceae; Listeria
+1718 Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Corynebacterineae; Corynebacteriaceae; Corynebacterium
+1719 Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Corynebacterineae; Corynebacteriaceae; Corynebacterium
+1764 Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Corynebacterineae; Mycobacteriaceae; Mycobacterium; Mycobacterium avium complex (MAC)
+1765 Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Corynebacterineae; Mycobacteriaceae; Mycobacterium; Mycobacterium tuberculosis complex
+1769 Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Corynebacterineae; Mycobacteriaceae; Mycobacterium
+1772 Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Corynebacterineae; Mycobacteriaceae; Mycobacterium
+1773 Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Corynebacterineae; Mycobacteriaceae; Mycobacterium; Mycobacterium tuberculosis complex
+1833 Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Corynebacterineae; Nocardiaceae; Rhodococcus
+1902 Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Streptomycineae; Streptomycetaceae; Streptomyces
+1916 Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Streptomycineae; Streptomycetaceae; Streptomyces
+2095 Bacteria; Firmicutes; Mollicutes; Mycoplasmataceae; Mycoplasma
+2097 Bacteria; Firmicutes; Mollicutes; Mycoplasmataceae; Mycoplasma
+2098 Bacteria; Firmicutes; Mollicutes; Mycoplasmataceae; Mycoplasma
+2130 Bacteria; Firmicutes; Mollicutes; Mycoplasmataceae; Ureaplasma
+2208 Archaea; Euryarchaeota; Methanomicrobia; Methanosarcinales; Methanosarcinaceae; Methanosarcina
+2209 Archaea; Euryarchaeota; Methanomicrobia; Methanosarcinales; Methanosarcinaceae; Methanosarcina
+2214 Archaea; Euryarchaeota; Methanomicrobia; Methanosarcinales; Methanosarcinaceae; Methanosarcina
+2234 Archaea; Euryarchaeota; Archaeoglobi; Archaeoglobales; Archaeoglobaceae; Archaeoglobus
+2238 Archaea; Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloarcula
+2247 Archaea; Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Halorubrum
+2261 Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae; Pyrococcus
+2287 Archaea; Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae; Sulfolobus
+2336 Bacteria; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga
+2371 Bacteria; Proteobacteria; Gammaproteobacteria; Xanthomonadales; Xanthomonadaceae; Xylella
+2711 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Sapindales; Rutaceae; Citrus
+2777 Eukaryota; Rhodophyta; Florideophyceae; Gracilariales; Gracilariaceae; Gracilaria
+2788 Eukaryota; Rhodophyta; Bangiophyceae; Bangiales; Bangiaceae; Porphyra
+2850 Eukaryota; stramenopiles; Bacillariophyta; Bacillariophyceae; Bacillariophycidae; Naviculales; Phaeodactylaceae; Phaeodactylum
+2903 Eukaryota; Haptophyceae; Isochrysidales; Emiliania
+2926 Eukaryota; Alveolata; Dinophyceae; Gonyaulacales; Gonyaulacaceae; Alexandrium
+2961 Eukaryota; Alveolata; Dinophyceae; Gymnodiniales; Gymnodiniaceae; Amphidinium
+2972 Eukaryota; Alveolata; Dinophyceae; Pyrocystales; Pyrocystis
+3012 Eukaryota; stramenopiles; Phaeophyceae; Fucales; Fucaceae; Fucus
+3046 Eukaryota; Viridiplantae; Chlorophyta; Chlorophyceae; Volvocales; Dunaliellaceae; Dunaliella
+3055 Eukaryota; Viridiplantae; Chlorophyta; Chlorophyceae; Volvocales; Chlamydomonadaceae; Chlamydomonas
+3190 Eukaryota; Viridiplantae; Chlorophyta; Prasinophyceae; Chlorodendrales; Chlorodendraceae; Scherffelia
+3197 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Marchantiophyta; Marchantiopsida; Marchantiidae; Marchantiales; Marchantiineae; Marchantiaceae; Marchantia
+3218 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Bryophyta; Bryopsida; Funariidae; Funariales; Funariaceae; Physcomitrella
+3225 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Bryophyta; Bryopsida; Dicranidae; Dicranales; Ditrichaceae; Ceratodon
+3311 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Ginkgophyta; Ginkgoales; Ginkgoaceae; Ginkgo
+3329 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Coniferopsida; Coniferales; Pinaceae; Picea
+3347 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Coniferopsida; Coniferales; Pinaceae; Pinus; Pinus
+3352 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Coniferopsida; Coniferales; Pinaceae; Pinus; Pinus
+3357 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Coniferopsida; Coniferales; Pinaceae; Pseudotsuga
+3369 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Coniferopsida; Coniferales; Cupressaceae; Cryptomeria
+3382 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Gnetophyta; Gnetopsida; Gnetales; Gnetaceae; Gnetum
+3467 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; Ranunculales; Papaveraceae; Eschscholzioideae; Eschscholzia
+3505 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fagales; Betulaceae; Betula
+3544 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Caryophyllales; Aizoaceae; Mesembryanthemum
+3562 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Caryophyllales; Amaranthaceae; Spinacia
+3570 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Caryophyllales; Caryophyllaceae; Dianthus
+3605 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; Vitaceae; Vitis
+3634 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Malvales; Malvaceae; Malvoideae; Gossypium
+3635 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Malvales; Malvaceae; Malvoideae; Gossypium
+3641 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Malvales; Malvaceae; Byttnerioideae; Theobroma
+3649 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Brassicales; Caricaceae; Carica
+3654 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Cucurbitales; Cucurbitaceae; Citrullus
+3656 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Cucurbitales; Cucurbitaceae; Cucumis
+3659 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Cucurbitales; Cucurbitaceae; Cucumis
+3693 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Malpighiales; Salicaceae; Saliceae; Populus
+3695 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Malpighiales; Salicaceae; Saliceae; Populus
+3702 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis
+3707 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Brassicales; Brassicaceae; Brassica
+3708 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Brassicales; Brassicaceae; Brassica
+3711 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Brassicales; Brassicaceae; Brassica
+3712 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Brassicales; Brassicaceae; Brassica
+3726 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Brassicales; Brassicaceae; Raphanus
+3747 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Rosales; Rosaceae; Rosoideae; Fragaria
+3750 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Rosales; Rosaceae; Maloideae; Malus
+3755 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Rosales; Rosaceae; Amygdaloideae; Prunus
+3760 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Rosales; Rosaceae; Amygdaloideae; Prunus
+3818 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Aeschynomeneae; Arachis
+3827 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Cicereae; Cicer
+3847 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Glycine
+3870 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Genisteae; Lupinus
+3873 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Genisteae; Lupinus
+3879 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Trifolieae; Medicago
+3880 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Trifolieae; Medicago
+3885 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Phaseolus
+3886 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Phaseolus
+3888 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Vicieae; Pisum
+3895 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Robinieae; Sesbania
+3899 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Trifolieae; Trifolium
+3906 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Vicieae; Vicia
+3917 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Vigna
+3981 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Malpighiales; Euphorbiaceae; Crotonoideae; Micrandreae; Hevea
+3983 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Malpighiales; Euphorbiaceae; Crotonoideae; Manihoteae; Manihot
+3988 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Malpighiales; Euphorbiaceae; Acalyphoideae; Acalypheae; Ricinus
+3993 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Malpighiales; Euphorbiaceae; Euphorbioideae; Euphorbieae; Euphorbia
+4006 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Malpighiales; Linaceae; Linum
+4039 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; campanulids; Apiales; Apiaceae; Apioideae; Scandiceae; Daucinae; Daucus
+4045 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; campanulids; Apiales; Apiaceae; Apioideae; apioid superclade; Apium clade; Apium
+4054 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; campanulids; Apiales; Araliaceae; Panax
+4072 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Solanales; Solanaceae; Capsicum
+4081 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Solanales; Solanaceae; Solanum; Lycopersicon
+4096 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Solanales; Solanaceae; Nicotiana
+4097 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Solanales; Solanaceae; Nicotiana
+4100 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Solanales; Solanaceae; Nicotiana
+4102 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Solanales; Solanaceae; Petunia
+4113 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Solanales; Solanaceae; Solanum
+4120 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Solanales; Convolvulaceae; Ipomoea
+4146 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Lamiales; Oleaceae; Olea
+4151 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Lamiales; Antirrhinaceae; Antirrhineae; Antirrhinum
+4182 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Lamiales; Pedaliaceae; Sesamum
+4232 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; campanulids; Asterales; Asteraceae; Asteroideae; Heliantheae; Helianthus
+4236 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; campanulids; Asterales; Asteraceae; Cichorioideae; Cichorieae; Lactuca
+4498 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; Pooideae; Aveneae; Avena
+4513 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; Pooideae; Triticeae; Hordeum
+4530 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; Ehrhartoideae; Oryzeae; Oryza
+4543 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACCAD clade; Panicoideae; Paniceae; Pennisetum
+4547 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACCAD clade; Panicoideae; Andropogoneae; Saccharum
+4550 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; Pooideae; Triticeae; Secale
+4558 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACCAD clade; Panicoideae; Andropogoneae; Sorghum
+4560 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACCAD clade; Panicoideae; Andropogoneae; Sorghum
+4565 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; Pooideae; Triticeae; Triticum
+4568 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; Pooideae; Triticeae; Triticum
+4571 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; Pooideae; Triticeae; Triticum
+4573 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; Pooideae; Triticeae; Aegilops
+4577 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACCAD clade; Panicoideae; Andropogoneae; Zea
+4641 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Zingiberales; Musaceae; Musa
+4679 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Asparagales; Alliaceae; Allium
+4682 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Asparagales; Alliaceae; Allium
+4686 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Asparagales; Asparagaceae; Asparagus
+4754 Eukaryota; Fungi; Ascomycota; Pneumocystidomycetes; Pneumocystidaceae; Pneumocystis
+4787 Eukaryota; stramenopiles; Oomycetes; Pythiales; Pythiaceae; Phytophthora
+4790 Eukaryota; stramenopiles; Oomycetes; Pythiales; Pythiaceae; Phytophthora
+4876 Eukaryota; Fungi; Glomeromycota; Glomeromycetes; Glomerales; Glomeraceae; Glomus
+4896 Eukaryota; Fungi; Ascomycota; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces
+4905 Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Pichia
+4911 Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Kluyveromyces
+4916 Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Kluyveromyces
+4920 Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Pichia
+4931 Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
+4932 Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
+4934 Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
+4952 Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Dipodascaceae; Yarrowia
+4956 Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Zygosaccharomyces
+4959 Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Debaryomyces
+5037 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Onygenales; Onygenaceae; Ajellomyces
+5059 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiales; Trichocomaceae; mitosporic Trichocomaceae; Aspergillus
+5061 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiales; Trichocomaceae; mitosporic Trichocomaceae; Aspergillus
+5062 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiales; Trichocomaceae; mitosporic Trichocomaceae; Aspergillus
+5068 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiales; Trichocomaceae; mitosporic Trichocomaceae; Aspergillus
+5085 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiales; Trichocomaceae; mitosporic Trichocomaceae; Aspergillus
+5116 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariomycetidae; Diaporthales; Valsaceae; Cryphonectria-Endothia complex; Cryphonectria
+5141 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariomycetidae; Sordariales; Sordariaceae; Neurospora
+5180 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Leotiomycetes; Helotiales; Sclerotiniaceae; Sclerotinia
+5207 Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Heterobasidiomycetes; Tremellomycetidae; Tremellales; Tremellaceae; Filobasidiella
+5270 Eukaryota; Fungi; Basidiomycota; Ustilaginomycetes; Ustilaginomycetidae; Ustilaginales; Ustilaginaceae; Ustilago
+5272 Eukaryota; Fungi; Basidiomycota; Urediniomycetes; Microbotryomycetidae; Microbotryales; Microbotryaceae; Microbotryum
+5306 Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Aphyllophorales; Corticiaceae; Phanerochaete
+5322 Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Agaricales; Pleurotaceae; Pleurotus
+5334 Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Agaricales; Schizophyllaceae; Schizophyllum
+5341 Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Agaricales; Agaricaceae; Agaricus
+5346 Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Agaricales; Psathyrellaceae; Coprinopsis
+5457 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariomycetes incertae sedis; Phyllachorales; Phyllachoraceae; Glomerella
+5466 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariomycetes incertae sedis; Phyllachorales; Phyllachoraceae; mitosporic Phyllachoraceae; Colletotrichum
+5476 Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; mitosporic Saccharomycetales; Candida
+5478 Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; mitosporic Saccharomycetales; Candida
+5482 Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; mitosporic Saccharomycetales; Candida
+5499 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Dothideomycetes et Chaetothyriomycetes incertae sedis; Mycosphaerellaceae; mitosporic Mycosphaerellaceae; Cladosporium
+5501 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Onygenales; mitosporic Onygenales; Coccidioides
+5507 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; mitosporic Hypocreales; Fusarium; Fusarium oxysporum complex
+5514 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; mitosporic Hypocreales; Fusarium
+5518 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; Nectriaceae; Gibberella
+5530 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; Clavicipitaceae; mitosporic Clavicipitaceae; Metarhizium
+5544 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; Hypocreaceae; Hypocrea
+5660 Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Leishmania; Leishmania braziliensis species complex
+5661 Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Leishmania
+5664 Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Leishmania
+5671 Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Leishmania
+5691 Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Trypanosoma
+5693 Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Trypanosoma; Schizotrypanum
+5722 Eukaryota; Parabasalidea; Trichomonadida; Trichomonadidae; Trichomonadinae; Trichomonas
+5741 Eukaryota; Diplomonadida; Hexamitidae; Giardiinae; Giardia
+5759 Eukaryota; Entamoebidae; Entamoeba
+5802 Eukaryota; Alveolata; Apicomplexa; Coccidia; Eimeriida; Eimeriidae; Eimeria
+5807 Eukaryota; Alveolata; Apicomplexa; Coccidia; Eimeriida; Cryptosporidiidae; Cryptosporidium
+5811 Eukaryota; Alveolata; Apicomplexa; Coccidia; Eimeriida; Sarcocystidae; Toxoplasma
+5821 Eukaryota; Alveolata; Apicomplexa; Haemosporida; Plasmodium
+5825 Eukaryota; Alveolata; Apicomplexa; Haemosporida; Plasmodium
+5833 Eukaryota; Alveolata; Apicomplexa; Haemosporida; Plasmodium
+5855 Eukaryota; Alveolata; Apicomplexa; Haemosporida; Plasmodium
+5861 Eukaryota; Alveolata; Apicomplexa; Haemosporida; Plasmodium
+5875 Eukaryota; Alveolata; Apicomplexa; Piroplasmida; Theileriidae; Theileria
+5888 Eukaryota; Alveolata; Ciliophora; Oligohymenophorea; Peniculida; Paramecium
+5911 Eukaryota; Alveolata; Ciliophora; Oligohymenophorea; Hymenostomatida; Tetrahymenina; Tetrahymena
+5932 Eukaryota; Alveolata; Ciliophora; Oligohymenophorea; Hymenostomatida; Ophryoglenina; Ichthyophthirius
+5936 Eukaryota; Alveolata; Ciliophora; Spirotrichea; Hypotrichia; Euplotida; Euplotidae; Moneuplotes
+6085 Eukaryota; Metazoa; Cnidaria; Hydrozoa; Hydroida; Anthomedusae; Hydridae; Hydra
+6100 Eukaryota; Metazoa; Cnidaria; Hydrozoa; Hydroida; Leptomedusae; Aequoreidae; Aequorea
+6161 Eukaryota; Metazoa; Platyhelminthes; Turbellaria; Seriata; Tricladida; Paludicola; Dugesiidae; Dugesia
+6182 Eukaryota; Metazoa; Platyhelminthes; Trematoda; Digenea; Strigeidida; Schistosomatoidea; Schistosomatidae; Schistosoma
+6183 Eukaryota; Metazoa; Platyhelminthes; Trematoda; Digenea; Strigeidida; Schistosomatoidea; Schistosomatidae; Schistosoma
+6204 Eukaryota; Metazoa; Platyhelminthes; Cestoda; Eucestoda; Cyclophyllidea; Taeniidae; Taenia
+6210 Eukaryota; Metazoa; Platyhelminthes; Cestoda; Eucestoda; Cyclophyllidea; Taeniidae; Echinococcus
+6211 Eukaryota; Metazoa; Platyhelminthes; Cestoda; Eucestoda; Cyclophyllidea; Taeniidae; Echinococcus
+6238 Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
+6239 Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
+6248 Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Panagrolaimoidea; Strongyloididae; Strongyloides
+6252 Eukaryota; Metazoa; Nematoda; Chromadorea; Ascaridida; Ascaridoidea; Ascarididae; Ascaris
+6253 Eukaryota; Metazoa; Nematoda; Chromadorea; Ascaridida; Ascaridoidea; Ascarididae; Ascaris
+6265 Eukaryota; Metazoa; Nematoda; Chromadorea; Ascaridida; Ascaridoidea; Toxocaridae; Toxocara
+6279 Eukaryota; Metazoa; Nematoda; Chromadorea; Spirurida; Filarioidea; Onchocercidae; Brugia
+6282 Eukaryota; Metazoa; Nematoda; Chromadorea; Spirurida; Filarioidea; Onchocercidae; Onchocerca
+6287 Eukaryota; Metazoa; Nematoda; Chromadorea; Spirurida; Filarioidea; Onchocercidae; Dirofilaria
+6289 Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Strongylida; Trichostrongyloidea; Haemonchidae; Haemonchinae; Haemonchus
+6293 Eukaryota; Metazoa; Nematoda; Chromadorea; Spirurida; Filarioidea; Onchocercidae; Wuchereria
+6303 Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Heteroderidae; Meloidogyninae; Meloidogyne
+6304 Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Heteroderidae; Meloidogyninae; Meloidogyne
+6305 Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Heteroderidae; Meloidogyninae; Meloidogyne
+6306 Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Heteroderidae; Meloidogyninae; Meloidogyne
+6317 Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Strongylida; Trichostrongyloidea; Haemonchidae; Ostertagiinae; Ostertagia
+6334 Eukaryota; Metazoa; Nematoda; Enoplea; Trichocephalida; Trichinellidae; Trichinella
+6500 Eukaryota; Metazoa; Mollusca; Gastropoda; Orthogastropoda; Apogastropoda; Heterobranchia; Euthyneura; Opisthobranchia; Anaspidea; Aplysioidea; Aplysiidae; Aplysia
+6526 Eukaryota; Metazoa; Mollusca; Gastropoda; Pulmonata; Basommatophora; Lymnaeoidea; Planorbidae; Biomphalaria
+6550 Eukaryota; Metazoa; Mollusca; Bivalvia; Pteriomorphia; Mytiloida; Mytiloidea; Mytilidae; Mytilus
+6551 Eukaryota; Metazoa; Mollusca; Bivalvia; Pteriomorphia; Mytiloida; Mytiloidea; Mytilidae; Mytilus
+6565 Eukaryota; Metazoa; Mollusca; Bivalvia; Pteriomorphia; Ostreoida; Ostreoidea; Ostreidae; Crassostrea
+6661 Eukaryota; Metazoa; Arthropoda; Crustacea; Branchiopoda; Anostraca; Artemiidae; Artemia
+6687 Eukaryota; Metazoa; Arthropoda; Crustacea; Malacostraca; Eumalacostraca; Eucarida; Decapoda; Dendrobranchiata; Penaeoidea; Penaeidae; Penaeus
+6689 Eukaryota; Metazoa; Arthropoda; Crustacea; Malacostraca; Eumalacostraca; Eucarida; Decapoda; Dendrobranchiata; Penaeoidea; Penaeidae; Litopenaeus
+6720 Eukaryota; Metazoa; Arthropoda; Crustacea; Malacostraca; Eumalacostraca; Eucarida; Decapoda; Pleocyemata; Astacidea; Astacoidea; Astacidae; Pacifastacus
+6941 Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Parasitiformes; Ixodida; Ixodidae; Boophilus
+6943 Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Parasitiformes; Ixodida; Ixodidae; Amblyomma
+6945 Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Parasitiformes; Ixodida; Ixodidae; Ixodes
+7029 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Hemiptera; Sternorrhyncha; Aphidiformes; Aphidoidea; Aphididae; Macrosiphini; Acyrthosiphon
+7038 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Hemiptera; Sternorrhyncha; Aleyrodiformes; Aleyrodoidea; Aleyrodidae; Aleyrodinae; Bemisia
+7070 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Cucujiformia; Tenebrionidae; Tribolium
+7091 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Bombycoidea; Bombycidae; Bombyx
+7092 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Bombycoidea; Bombycidae; Bombyx
+7111 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Plusiinae; Trichoplusia
+7121 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Bombycoidea; Saturniidae; Saturniinae; Saturniini; Antheraea
+7130 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Sphingiodea; Sphingidae; Sphinginae; Manduca
+7159 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Culicoidea; Aedes; Stegomyia
+7165 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Culicoidea; Anopheles
+7173 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Culicoidea; Anopheles
+7175 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Culicoidea; Culex; Culex
+7200 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Psychodoidea; Psychodidae; Lutzomyia; Lutzomyia
+7213 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Tephritoidea; Tephritidae; Ceratitis
+7217 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
+7226 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
+7227 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
+7229 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
+7234 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
+7237 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
+7240 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
+7241 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
+7244 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
+7245 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
+7264 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
+7368 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Muscoidea; Muscidae; Haematobia
+7370 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Muscoidea; Muscidae; Musca
+7394 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Hippoboscoidea; Glossinidae; Glossina
+7460 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Apidae; Apis
+7515 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Siphonaptera; Pulicidae; Pulicinae; Ctenocephalides
+7634 Eukaryota; Metazoa; Echinodermata; Eleutherozoa; Echinozoa; Echinoidea; Euechinoidea; Echinacea; Echinoida; Echinometridae; Heliocidaris
+7650 Eukaryota; Metazoa; Echinodermata; Eleutherozoa; Echinozoa; Echinoidea; Euechinoidea; Echinacea; Echinoida; Strongylocentrotidae; Hemicentrotus
+7668 Eukaryota; Metazoa; Echinodermata; Eleutherozoa; Echinozoa; Echinoidea; Euechinoidea; Echinacea; Echinoida; Strongylocentrotidae; Strongylocentrotus
+7719 Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona; Phlebobranchia; Cionidae; Ciona
+7723 Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Stolidobranchia; Styelidae; Polyandrocarpa
+7729 Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Stolidobranchia; Pyuridae; Halocynthia
+7739 Eukaryota; Metazoa; Chordata; Cephalochordata; Branchiostomidae; Branchiostoma
+7741 Eukaryota; Metazoa; Chordata; Cephalochordata; Branchiostomidae; Branchiostoma
+7757 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Hyperoartia; Petromyzontiformes; Petromyzontidae; Petromyzon
+7801 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Chondrichthyes; Elasmobranchii; Galeomorphii; Galeoidea; Orectolobiformes; Ginglymostomatidae; Ginglymostoma
+7937 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Anguilliformes; Anguillidae; Anguilla
+7955 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Cyprinidae; Danio
+7957 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Cyprinidae; Carassius
+7959 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Cyprinidae; Ctenopharyngodon
+7962 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Cyprinidae; Cyprinus
+7998 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Siluriformes; Ictaluridae; Ictalurus
+8018 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Protacanthopterygii; Salmoniformes; Salmonidae; Oncorhynchus
+8022 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Protacanthopterygii; Salmoniformes; Salmonidae; Oncorhynchus
+8023 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Protacanthopterygii; Salmoniformes; Salmonidae; Oncorhynchus
+8030 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Protacanthopterygii; Salmoniformes; Salmonidae; Salmo
+8032 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Protacanthopterygii; Salmoniformes; Salmonidae; Salmo
+8036 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Protacanthopterygii; Salmoniformes; Salmonidae; Salvelinus
+8049 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Paracanthopterygii; Gadiformes; Gadidae; Gadus
+8078 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Atherinomorpha; Cyprinodontiformes; Fundulidae; Fundulus
+8081 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Atherinomorpha; Cyprinodontiformes; Poeciliidae; Poecilia
+8090 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Atherinomorpha; Beloniformes; Adrianichthyidae; Oryziinae; Oryzias
+8128 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Labroidei; Cichlidae; Oreochromis
+8150 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Labroidei; Cichlidae; Tropheus
+8161 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Carangoidei; Carangidae; Seriola
+8175 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Percoidei; Sparidae; Sparus
+8222 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Gobioidei; Gobiidae; Gillichthys
+8245 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Scombroidei; Xiphiidae; Xiphias
+8255 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Pleuronectiformes; Pleuronectoidei; Paralichthyidae; Paralichthys
+8260 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Pleuronectiformes; Pleuronectoidei; Pleuronectidae; Platichthys
+8262 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Pleuronectiformes; Pleuronectoidei; Pleuronectidae; Pleuronectes
+8265 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Pleuronectiformes; Pleuronectoidei; Pleuronectidae; Pseudopleuronectes
+8267 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Pleuronectiformes; Pleuronectoidei; Pleuronectidae; Hippoglossus
+8296 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Batrachia; Caudata; Salamandroidea; Ambystomatidae; Ambystoma
+8355 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Batrachia; Anura; Mesobatrachia; Pipoidea; Pipidae; Xenopodinae; Xenopus
+8364 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Batrachia; Anura; Mesobatrachia; Pipoidea; Pipidae; Xenopodinae; Silurana
+8400 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Batrachia; Anura; Neobatrachia; Ranoidea; Ranidae; Rana; Aquarana
+8723 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Lepidosauria; Squamata; Scleroglossa; Serpentes; Colubroidea; Viperidae; Crotalinae; Bothrops
+8801 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Palaeognathae; Struthioniformes; Struthionidae; Struthio
+8839 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Anseriformes; Anatidae; Anas
+8932 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Columbiformes; Columbidae; Columba
+9031 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Galliformes; Phasianidae; Phasianinae; Gallus
+9091 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Galliformes; Phasianidae; Phasianinae; Coturnix
+9103 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Galliformes; Phasianidae; Meleagris
+9157 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Passeriformes; Paridae; Parus
+9238 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Sphenisciformes; Spheniscidae; Pygoscelis
+9258 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Monotremata; Ornithorhynchidae; Ornithorhynchus
+9315 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Metatheria; Diprotodontia; Macropodidae; Macropus
+9337 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Metatheria; Diprotodontia; Phalangeridae; Trichosurus
+9361 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Edentata; Dasypodidae; Dasypus
+9438 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Chiroptera; Microchiroptera; Molossidae; Tadarida
+9447 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Strepsirhini; Lemuridae; Lemur
+9483 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Platyrrhini; Callitrichidae; Callithrix
+9490 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Platyrrhini; Callitrichidae; Saguinus
+9509 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Platyrrhini; Cebidae; Atelinae; Ateles
+9521 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Platyrrhini; Cebidae; Cebinae; Saimiri
+9534 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Cercopithecidae; Cercopithecinae; Cercopithecus
+9541 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Cercopithecidae; Cercopithecinae; Macaca
+9542 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Cercopithecidae; Cercopithecinae; Macaca
+9544 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Cercopithecidae; Cercopithecinae; Macaca
+9545 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Cercopithecidae; Cercopithecinae; Macaca
+9555 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Cercopithecidae; Cercopithecinae; Papio
+9557 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Cercopithecidae; Cercopithecinae; Papio
+9580 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hylobatidae; Hylobates
+9593 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Gorilla
+9597 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Pan
+9598 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Pan
+9600 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Pongo
+9606 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo
+9615 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Carnivora; Fissipedia; Canidae; Canis
+9644 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Carnivora; Fissipedia; Ursidae; Ursus
+9660 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Carnivora; Fissipedia; Mustelidae; Mustelinae; Martes
+9685 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Carnivora; Fissipedia; Felidae; Felis
+9720 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Carnivora; Pinnipedia; Phocidae; Phoca
+9783 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Proboscidea; Elephantidae; Elephas
+9785 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Proboscidea; Elephantidae; Loxodonta
+9796 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Perissodactyla; Equidae; Equus
+9823 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Cetartiodactyla; Suina; Suidae; Sus
+9838 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Cetartiodactyla; Tylopoda; Camelidae; Camelus
+9844 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Cetartiodactyla; Tylopoda; Camelidae; Lama
+9860 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Cetartiodactyla; Ruminantia; Pecora; Cervoidea; Cervidae; Cervinae; Cervus
+9870 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Cetartiodactyla; Ruminantia; Pecora; Cervoidea; Cervidae; Odocoileinae; Rangifer
+9897 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Cetartiodactyla; Ruminantia; Pecora; Bovoidea; Bovidae; Aepycerotinae; Aepyceros
+9913 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Cetartiodactyla; Ruminantia; Pecora; Bovoidea; Bovidae; Bovinae; Bos
+9915 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Cetartiodactyla; Ruminantia; Pecora; Bovoidea; Bovidae; Bovinae; Bos
+9925 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Cetartiodactyla; Ruminantia; Pecora; Bovoidea; Bovidae; Caprinae; Capra
+9940 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Cetartiodactyla; Ruminantia; Pecora; Bovoidea; Bovidae; Caprinae; Ovis
+9970 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Cetartiodactyla; Ruminantia; Pecora; Bovoidea; Bovidae; Bovinae; Syncerus
+9986 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Lagomorpha; Leporidae; Oryctolagus
+9995 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Sciuridae; Sciurinae; Marmota
+10029 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Cricetinae; Cricetulus
+10036 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Cricetinae; Mesocricetus
+10041 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Sigmodontinae; Peromyscus
+10042 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Sigmodontinae; Peromyscus
+10047 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Gerbillinae; Meriones
+10090 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Mus
+10096 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Mus
+10116 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus
+10117 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus
+10129 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Apodemus
+10141 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Hystricognathi; Caviidae; Cavia
+10245 Viruses; dsDNA viruses, no RNA stage; Poxviridae; Chordopoxvirinae; Orthopoxvirus
+10298 Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Alphaherpesvirinae; Simplexvirus
+10335 Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Alphaherpesvirinae; Varicellovirus
+10345 Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Alphaherpesvirinae; Varicellovirus
+10359 Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Betaherpesvirinae; Cytomegalovirus
+10376 Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Gammaherpesvirinae; Lymphocryptovirus
+10407 Viruses; Retroid viruses; Hepadnaviridae; Orthohepadnavirus
+10497 Viruses; dsDNA viruses, no RNA stage; Asfarviridae; Asfivirus
+10566 Viruses; dsDNA viruses, no RNA stage; Papillomaviridae; Papillomavirus
+10581 Viruses; dsDNA viruses, no RNA stage; Papillomaviridae; Papillomavirus
+10632 Viruses; dsDNA viruses, no RNA stage; Polyomaviridae; Polyomavirus
+10633 Viruses; dsDNA viruses, no RNA stage; Polyomaviridae; Polyomavirus
+10760 Viruses; dsDNA viruses, no RNA stage; Caudovirales; Podoviridae; T7-like viruses
+10798 Viruses; ssDNA viruses; Parvoviridae; Parvovirinae; Erythrovirus
+10995 Viruses; dsRNA viruses; Birnaviridae; Avibirnavirus
+11034 Viruses; ssRNA positive-strand viruses, no DNA stage; Togaviridae; Alphavirus; WEEV complex
+11041 Viruses; ssRNA positive-strand viruses, no DNA stage; Togaviridae; Rubivirus
+11047 Viruses; ssRNA positive-strand viruses, no DNA stage; Nidovirales; Arteriviridae; Arterivirus
+11072 Viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; Flavivirus; Japanese encephalitis virus group
+11082 Viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; Flavivirus; Japanese encephalitis virus group
+11099 Viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; Pestivirus
+11103 Viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; Hepacivirus
+11120 Viruses; ssRNA positive-strand viruses, no DNA stage; Nidovirales; Coronaviridae; Coronavirus
+11161 Viruses; ssRNA negative-strand viruses; Mononegavirales; Paramyxoviridae; Paramyxovirinae; Rubulavirus
+11176 Viruses; ssRNA negative-strand viruses; Mononegavirales; Paramyxoviridae; Paramyxovirinae; Rubulavirus
+11234 Viruses; ssRNA negative-strand viruses; Mononegavirales; Paramyxoviridae; Paramyxovirinae; Morbillivirus
+11246 Viruses; ssRNA negative-strand viruses; Mononegavirales; Paramyxoviridae; Pneumovirinae; Pneumovirus
+11250 Viruses; ssRNA negative-strand viruses; Mononegavirales; Paramyxoviridae; Pneumovirinae; Pneumovirus
+11264 Viruses; ssRNA negative-strand viruses; Mononegavirales; Paramyxoviridae; Pneumovirinae; Metapneumovirus
+11276 Viruses; ssRNA negative-strand viruses; Mononegavirales; Rhabdoviridae; Vesiculovirus
+11292 Viruses; ssRNA negative-strand viruses; Mononegavirales; Rhabdoviridae; Lyssavirus
+11660 Viruses; Retroid viruses; Retroviridae; Lentivirus; Ovine/caprine lentivirus
+11665 Viruses; Retroid viruses; Retroviridae; Lentivirus; Equine lentiviruses
+11673 Viruses; Retroid viruses; Retroviridae; Lentivirus; Feline lentiviruses
+11676 Viruses; Retroid viruses; Retroviridae; Lentivirus; Primate lentivirus group
+11709 Viruses; Retroid viruses; Retroviridae; Lentivirus; Primate lentivirus group
+11723 Viruses; Retroid viruses; Retroviridae; Lentivirus; Primate lentivirus group
+11768 Viruses; Retroid viruses; Retroviridae; Gammaretrovirus
+11786 Viruses; Retroid viruses; Retroviridae; Gammaretrovirus
+11827 Viruses; Retroid viruses; Retroviridae
+11886 Viruses; Retroid viruses; Retroviridae; Alpharetrovirus
+11966 Viruses; Retroid viruses; Retroviridae
+11983 Viruses; ssRNA positive-strand viruses, no DNA stage; Caliciviridae; Norovirus
+12092 Viruses; ssRNA positive-strand viruses, no DNA stage; Picornaviridae; Hepatovirus
+12111 Viruses; ssRNA positive-strand viruses, no DNA stage; Picornaviridae; Aphthovirus; Foot-and-mouth disease virus
+12118 Viruses; ssRNA positive-strand viruses, no DNA stage; Picornaviridae; Aphthovirus; Foot-and-mouth disease virus
+12162 Viruses; ssRNA positive-strand viruses, no DNA stage; Closteroviridae; Closterovirus
+12216 Viruses; ssRNA positive-strand viruses, no DNA stage; Potyviridae; Potyvirus
+12230 Viruses; ssRNA positive-strand viruses, no DNA stage; Potyviridae; Potyvirus
+12232 Viruses; ssRNA positive-strand viruses, no DNA stage; Potyviridae; Potyvirus
+12305 Viruses; ssRNA positive-strand viruses, no DNA stage; Bromoviridae; Cucumovirus
+12461 Viruses; ssRNA positive-strand viruses, no DNA stage; Hepatitis E-like viruses
+12475 Viruses; Deltavirus
+12637 Viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; Flavivirus; Dengue virus group
+12702 Viruses; ssRNA positive-strand viruses, no DNA stage; Astroviridae; Mamastrovirus
+12721 Viruses; Retroid viruses; Retroviridae; Lentivirus; Primate lentivirus group
+12814 Viruses; ssRNA negative-strand viruses; Mononegavirales; Paramyxoviridae; Pneumovirinae; Pneumovirus
+13323 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Scombroidei; Scombridae; Acanthocybium
+13333 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; stem Magnoliophyta; Amborellaceae; Amborella
+13443 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Gentianales; Rubiaceae; Ixoroideae; Coffeeae; Coffea
+13489 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Percoidei; Moronidae; Dicentrarchus
+13515 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Strepsirhini; Lemuridae; Eulemur
+13563 Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Agaricales; Schizophyllaceae; Heterobasidion; Heterobasidion annosum species complex
+13616 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Metatheria; Didelphimorphia; Didelphidae; Monodelphis
+13773 Archaea; Crenarchaeota; Thermoprotei; Thermoproteales; Thermoproteaceae; Pyrobaculum
+23211 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Rosales; Rosaceae; Maloideae; Pyrus
+27288 Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
+27291 Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
+27293 Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
+27294 Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
+27337 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; mitosporic Hypocreales; Verticillium
+27405 Eukaryota; Metazoa; Arthropoda; Crustacea; Malacostraca; Eumalacostraca; Eucarida; Decapoda; Dendrobranchiata; Penaeoidea; Penaeidae; Marsupenaeus
+27689 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Chondrostei; Acipenseriformes; Acipenseridae; Acipenser
+27828 Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Strongylida; Trichostrongyloidea; Cooperiidae; Cooperia
+27835 Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Strongylida; Trichostrongyloidea; Heligmonellidae; Nippostrongylinae; Nippostrongylus
+27923 Eukaryota; Metazoa; Ctenophora; Cyclocoela; Lobata; Bolinopsidae; Mnemiopsis
+28037 Bacteria; Firmicutes; Lactobacillales; Streptococcaceae; Streptococcus
+28232 Bacteria; Proteobacteria; Deltaproteobacteria; Desulfuromonadales; Geobacteraceae; Geobacter
+28344 Viruses; ssRNA positive-strand viruses, no DNA stage; Nidovirales; Arteriviridae; Arterivirus
+28450 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Burkholderia; pseudomallei group
+28526 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Solanales; Solanaceae; Solanum; Lycopersicon
+28532 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Brassicales; Brassicaceae; Cleome
+28610 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Tephritoidea; Tephritidae; Rhagoletis
+28875 Viruses; dsRNA viruses; Reoviridae; Rotavirus
+28901 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Salmonella
+28909 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACCAD clade; Chloridoideae; Cynodonteae; Cynodon
+28985 Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Kluyveromyces
+29058 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Heliothinae; Helicoverpa
+29158 Eukaryota; Metazoa; Mollusca; Bivalvia; Pteriomorphia; Mytiloida; Mytiloidea; Mytilidae; Mytilus
+29159 Eukaryota; Metazoa; Mollusca; Bivalvia; Pteriomorphia; Ostreoida; Ostreoidea; Ostreidae; Crassostrea
+29170 Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Strongylida; Ancylostomatoidea; Ancylostomatidae; Ancylostomatinae; Ancylostoma
+29176 Eukaryota; Alveolata; Apicomplexa; Coccidia; Eimeriida; Sarcocystidae; Neospora
+29449 Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Rhizobiaceae; Rhizobium/Agrobacterium group; Rhizobium
+29459 Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Brucellaceae; Brucella
+29471 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Pectobacterium
+29488 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Photorhabdus
+29501 Bacteria; Firmicutes; Mollicutes; Mycoplasmataceae; Mycoplasma
+29518 Bacteria; Spirochaetes; Spirochaetales; Spirochaetaceae; Borrelia; Borrelia burgdorferi group
+29519 Bacteria; Spirochaetes; Spirochaetales; Spirochaetaceae; Borrelia; Borrelia burgdorferi group
+29546 Bacteria; Proteobacteria; Deltaproteobacteria; Desulfovibrionales; Desulfovibrionaceae; Lawsonia
+29729 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Malvales; Malvaceae; Malvoideae; Gossypium
+29730 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Malvales; Malvaceae; Malvoideae; Gossypium
+29760 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; Vitaceae; Vitis
+29883 Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Agaricales; Tricholomataceae; Laccaria
+30286 Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Stolidobranchia; Molgulidae; Molgula
+30301 Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Stolidobranchia; Botryllidae; Botryllus
+31033 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Tetraodontiformes; Tetradontoidea; Tetraodontidae; Takifugu
+31199 Eukaryota; Metazoa; Mollusca; Bivalvia; Pteriomorphia; Pectinoida; Pectinoidea; Pectinidae; Argopecten
+31216 Eukaryota; Metazoa; Mollusca; Gastropoda; Orthogastropoda; Apogastropoda; Caenogastropoda; Sorbeoconcha; Hypsogastropoda; Littorinimorpha; Littorinoidea; Littorinidae; Littorina
+31243 Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Heteroderidae; Heteroderinae; Globodera
+32538 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Carnivora; Fissipedia; Felidae; Leopardus
+33085 Eukaryota; Entamoebidae; Entamoeba
+33169 Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Eremothecium
+33178 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiales; Trichocomaceae; mitosporic Trichocomaceae; Aspergillus
+34245 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; campanulids; Asterales; Asteraceae; Asteroideae; Heliantheae; Zinnia
+34256 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Lamiales; Lamiaceae; Nepetoideae; Mentheae; Mentha
+34274 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Malvales; Malvaceae; Malvoideae; Gossypium
+34317 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; Myrtales; Myrtaceae; Eucalyptus
+34358 Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
+34373 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Leotiomycetes; Erysiphales; Erysiphaceae; Blumeria
+34488 Eukaryota; Fungi; Zygomycota; Zygomycetes; Entomophthorales; Ancylistaceae; Conidiobolus
+34506 Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Panagrolaimoidea; Strongyloididae; Strongyloides
+34594 Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Parasitiformes; Ixodida; Argasidae; Ornithodoros
+34610 Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Parasitiformes; Ixodida; Ixodidae; Amblyomma
+34740 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Papilionoidea; Nymphalidae; Heliconiinae; Heliconius
+34765 Eukaryota; Metazoa; Chordata; Urochordata; Appendicularia; Oikopleuridae; Oikopleura
+34816 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Percoidei; Moronidae; Morone
+35520 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACCAD clade; Panicoideae; Paniceae; Pennisetum
+35632 Eukaryota; Metazoa; Annelida; Clitellata; Oligochaeta; Haplotaxida; Lumbricina; Lumbricidae; Lumbricus
+35845 Eukaryota; Viridiplantae; Chlorophyta; Ulvophyceae; Dasycladales; Dasycladaceae; Acetabularia
+35876 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Asparagales; Iridaceae; Iris
+35883 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Solanales; Convolvulaceae; Ipomoea
+35884 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Solanales; Convolvulaceae; Ipomoea
+35938 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Robinieae; Robinia
+36090 Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Heteroderidae; Heteroderinae; Globodera
+36452 Viruses; dsDNA viruses, no RNA stage; Herpesviridae; unclassified Herpesviridae; stealth viruses
+36596 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Rosales; Rosaceae; Amygdaloideae; Prunus
+36825 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Orthopteroidea; Phasmatodea; Euphasmida; Phyllioidea; Bacillidae; Bacillus
+37293 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Platyrrhini; Cebidae; Aotinae; Aotus
+37296 Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Gammaherpesvirinae; Rhadinovirus
+37468 Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Boletales; Sclerodermatineae; Pisolithaceae; Pisolithus
+37656 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Sapindales; Rutaceae; Citrus
+37657 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Caryophyllales; Caryophyllaceae; Silene
+37682 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; Pooideae; Triticeae; Aegilops
+37690 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Sapindales; Rutaceae; Poncirus
+37727 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiales; Trichocomaceae; mitosporic Trichocomaceae; Penicillium
+37769 Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Heterobasidiomycetes; Tremellomycetidae; Tremellales; Tremellaceae; Filobasidiella
+38033 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariomycetidae; Sordariales; Chaetomiaceae; Chaetomium
+38249 Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Trypanosoma
+38666 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Heteromyidae; Perognathinae; Chaetodipus
+38937 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Lepidosauria; Squamata; Iguania; Iguanidae; Polychrotinae; Anolis
+39984 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Malpighiales; Rhizophoraceae; Bruguiera
+40051 Viruses; dsRNA viruses; Reoviridae; Orbivirus
+40352 Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Strongylida; Trichostrongyloidea; Trichostrongylidae; Trichostrongylinae; Trichostrongylus
+40366 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
+40559 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Leotiomycetes; Helotiales; Sclerotiniaceae; Botryotinia
+40686 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Malpighiales; Salicaceae; Saliceae; Salix
+40930 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Hemiptera; Sternorrhyncha; Aphidiformes; Coccoidea; Pseudococcidae; Planococcus
+40932 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Hemiptera; Sternorrhyncha; Aphidiformes; Aphidoidea; Aphididae; Aphidini; Rhopalosiphum
+41429 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Culicoidea; Anopheles
+42156 Eukaryota; Metazoa; Nematoda; Chromadorea; Spirurida; Filarioidea; Onchocercidae; Litomosoides
+42251 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Pezizomycetes; Pezizales; Tuberaceae; Tuber
+42329 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Cycadophyta; Cycadales; Zamiaceae; Zamia
+42439 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Brassicales; Limnanthaceae; Limnanthes
+42677 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; Nectriaceae; Gibberella; Gibberella fujikuroi complex
+42890 Eukaryota; Alveolata; Apicomplexa; Coccidia; Eimeriida; Sarcocystidae; Sarcocystis
+43114 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Batrachia; Caudata; Salamandroidea; Ambystomatidae; Ambystoma
+43425 Eukaryota; Fungi; Glomeromycota; Glomeromycetes; Glomerales; Glomeraceae; Glomus
+43928 Archaea; Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Halobaculum
+44015 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Glycine
+44689 Eukaryota; Mycetozoa; Dictyosteliida; Dictyostelium
+45249 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis
+45464 Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Strongylida; Trichostrongyloidea; Haemonchidae; Ostertagiinae; Teladorsagia
+45687 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Glycine
+45929 Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Pratylenchidae; Pratylenchinae; Pratylenchus
+45954 Eukaryota; Metazoa; Mollusca; Bivalvia; Heteroconchia; Veneroida; Dreissenoidea; Dreissenidae; Dreissena
+46761 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Batrachia; Caudata; Salamandroidea; Plethodontidae; Plethodon
+47247 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Loteae; Lotus
+47664 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Malpighiales; Salicaceae; Saliceae; Populus
+47834 Bacteria; Firmicutes; Mollicutes; Entomoplasmatales; Spiroplasmataceae; Spiroplasma
+47853 Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Micromonosporineae; Micromonosporaceae; Micromonospora
+48215 Eukaryota; Metazoa; Platyhelminthes; Trematoda; Digenea; Echinostomida; Echinostomata; Echinostomatidae; Echinostoma
+48935 Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Novosphingobium
+49338 Bacteria; Firmicutes; Clostridia; Clostridiales; Peptococcaceae; Desulfitobacterium
+49351 Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Cephaloboidea; Cephalobidae; Zeldia
+49451 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Solanales; Solanaceae; Nicotiana
+49495 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Moniliformopses; Filicophyta; Filicopsida; Filicales; Pteridaceae; Ceratopteris
+51029 Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Heteroderidae; Heteroderinae; Heterodera
+51031 Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Strongylida; Ancylostomatoidea; Ancylostomatidae; Bunostominae; Necator
+51240 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fagales; Juglandaceae; Juglans
+51453 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; Hypocreaceae; Hypocrea
+51511 Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona; Phlebobranchia; Cionidae; Ciona
+51657 Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Kluyveromyces
+52283 Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Acariformes; Sarcoptiformes; Astigmata; Psoroptidia; Sarcoptoidea; Sarcoptidae; Sarcoptes
+52714 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; Pooideae; Triticeae; Leymus
+52792 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Passeriformes; Turdidae; Luscinia
+53326 Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Strongylida; Ancylostomatoidea; Ancylostomatidae; Ancylostomatinae; Ancylostoma
+53413 Bacteria; Proteobacteria; Gammaproteobacteria; Xanthomonadales; Xanthomonadaceae; Xanthomonas
+54126 Eukaryota; Metazoa; Nematoda; Chromadorea; Diplogasterida; Neodiplogasteridae; Pristionchus
+54290 Viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; GBV-C/HGV group
+54314 Viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; Pestivirus
+54672 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Malpighiales; Euphorbiaceae; Euphorbioideae; Euphorbieae; Euphorbia
+54734 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Dothideomycetes et Chaetothyriomycetes incertae sedis; Mycosphaerellaceae; Mycosphaerella
+55088 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Orthopteroidea; Phasmatodea; Euphasmida; Phyllioidea; Bacillidae; Bacillus
+55188 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Sapindales; Rutaceae; Citrus
+55529 Eukaryota; Cryptophyta; Cryptomonadaceae; Guillardia
+55670 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; campanulids; Asterales; Asteraceae; Asteroideae; Eupatorieae; Stevia
+55987 Viruses; ssRNA negative-strand viruses; Orthomyxoviridae; unclassified Orthomyxoviridae
+57667 Viruses; Retroid viruses; Retroviridae; Lentivirus; Primate lentivirus group
+57870 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Orthopteroidea; Phasmatodea; Euphasmida; Phyllioidea; Bacillidae; Bacillus
+58002 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Hemiptera; Sternorrhyncha; Aphidiformes; Phylloxeroidea; Phylloxeridae; Daktulosphaira
+58031 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Cycadophyta; Cycadales; Cycadaceae; Cycas
+59479 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Chiroptera; Microchiroptera; Rhinolophidae; Rhinolophinae; Rhinolophus
+59689 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis
+59747 Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Heteroderidae; Meloidogyninae; Meloidogyne
+59777 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Lycopodiophyta; Isoetopsida; Selaginellales; Selaginellaceae; Selaginella
+59861 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Protacanthopterygii; Salmoniformes; Salmonidae; Coregonus
+61147 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Malpighiales; Rhizophoraceae; Kandelia
+62324 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Culicoidea; Anopheles
+62890 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Solanales; Solanaceae; Solanum; Lycopersicon
+63629 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; Ehrhartoideae; Oryzeae; Oryza
+63737 Bacteria; Cyanobacteria; Nostocales; Nostocaceae; Nostoc
+64091 Archaea; Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Halobacterium
+64093 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Lamiales; Orobanchaceae; Rhinantheae; Triphysaria
+64391 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Cucujiformia; Phytophaga; Chrysomeloidea; Chrysomelidae; Bruchinae; Bruchini; Callosobruchus
+64468 Eukaryota; Metazoa; Arthropoda; Crustacea; Malacostraca; Eumalacostraca; Eucarida; Decapoda; Dendrobranchiata; Penaeoidea; Penaeidae; Litopenaeus
+64602 Archaea; Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Natrialba
+64679 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Sciuridae; Sciurinae; Tamias
+64717 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Arvicolinae; Microtus
+65661 Eukaryota; Acanthamoebidae; Acanthamoeba
+66189 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Testudines; Cryptodira; Testudinoidea; Testudinidae; Geochelone
+66913 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Siluriformes; Ictaluridae; Ictalurus
+67593 Eukaryota; stramenopiles; Oomycetes; Pythiales; Pythiaceae; Phytophthora
+68887 Viruses; ssDNA viruses; Circoviridae; Anellovirus
+69266 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; Ericales; Ericaceae; Vaccinioideae; Vaccinieae; Vaccinium
+69293 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Gasterosteiformes; Gasterosteidae; Gasterosteus
+70415 Eukaryota; Metazoa; Nematoda; Enoplea; Trichocephalida; Trichuridae; Trichuris
+70448 Eukaryota; Viridiplantae; Chlorophyta; Prasinophyceae; Mamiellales; Mamiellaceae; Ostreococcus
+70863 Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Alteromonadaceae; Shewanella
+71139 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; Myrtales; Myrtaceae; Eucalyptus
+71150 Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Boletales; Paxilineae; Paxillaceae; Paxillus
+71223 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Elateriformia; Cantharoidea; Lampyridae; Pyrocoelia
+71647 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Coniferopsida; Coniferales; Pinaceae; Pinus; Pinus
+72088 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Scorpaeniformes; Scorpaenoidei; Scorpaenidae; Sebastes
+73107 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Gruiformes; Otididae; Otis
+73234 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Orthopteroidea; Phasmatodea; Euphasmida; Phyllioidea; Bacillidae; Bacillus
+73275 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; campanulids; Asterales; Asteraceae; Asteroideae; Heliantheae; Helianthus
+73304 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; campanulids; Asterales; Asteraceae; Asteroideae; Heliantheae; Helianthus
+73824 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Malpighiales; Salicaceae; Saliceae; Populus
+74081 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Lepidosauria; Squamata; Scleroglossa; Scincomorpha; Lacertoidea; Lacertidae; Podarcis
+74649 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Rosales; Rosaceae; Rosoideae; Rosa
+74940 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Protacanthopterygii; Salmoniformes; Salmonidae; Oncorhynchus
+75846 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Anseriformes; Anatidae; Anas
+75943 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; campanulids; Asterales; Asteraceae; Cichorioideae; Cichorieae; Lactuca
+76149 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Caryophyllales; Plumbaginaceae; Plumbago
+76340 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Percoidei; Sciaenidae; Sciaenops
+76593 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Cyprinidae; Acrossocheilus
+76867 Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Agaricales; Cortinariaceae; Hebeloma
+77108 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; stem Magnoliophyta; Nymphaeaceae; Nuphar
+78584 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Strepsirhini; Megaladapidae; Lepilemur
+79327 Eukaryota; Metazoa; Platyhelminthes; Turbellaria; Seriata; Tricladida; Paludicola; Dugesiidae; Schmidtea
+79517 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Cucujiformia; Phytophaga; Chrysomeloidea; Chrysomelidae; Chrysomelinae; Timarchini; Timarcha
+79880 Bacteria; Firmicutes; Bacillales; Bacillaceae; Bacillus
+79923 Eukaryota; Metazoa; Platyhelminthes; Trematoda; Digenea; Opisthorchiida; Opisthorchiata; Opisthorchioidea; Opisthorchiidae; Clonorchis
+80365 Eukaryota; stramenopiles; Phaeophyceae; Laminariales; Laminariaceae; Laminaria
+80379 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Solanales; Solanaceae; Capsicum
+80863 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Malpighiales; Salicaceae; Saliceae; Populus
+82528 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Asparagales; Iridaceae; Crocus
+82927 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Lamiales; Acanthaceae; Acanthaceae incertae sedis; Avicennia
+83288 Eukaryota; Rhodophyta; Florideophyceae; Ceramiales; Ceramiaceae; Griffithsia
+83558 Bacteria; Chlamydiae; Chlamydiales; Chlamydiaceae; Chlamydophila
+83675 Eukaryota; Alveolata; Apicomplexa; Coccidia; Eimeriida; Sarcocystidae; Neospora
+83912 Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Acariformes; Sarcoptiformes; Astigmata; Psoroptidia; Sarcoptoidea; Psoroptidae; Psoroptes
+84072 Eukaryota; Metazoa; Platyhelminthes; Turbellaria; Acoelomorpha; Acoela; Sagittiferidae; Symsagittifera
+85571 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Sapindales; Rutaceae; Citrus
+86005 Bacteria; Firmicutes; Bacillales; Alicyclobacillaceae; Pasteuria
+86304 Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales; Alteromonadaceae; Microbulbifer
+87841 Eukaryota; Metazoa; Mollusca; Gastropoda; Pulmonata; Stylommatophora; Sigmurethra; Helicoidea; Bradybaenidae; Euhadra
+89411 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Brassicales; Brassicaceae; Descurainia
+89462 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Cetartiodactyla; Ruminantia; Pecora; Bovoidea; Bovidae; Bovinae; Bubalus
+92652 Viruses; dsDNA viruses, no RNA stage; Nimaviridae; Whispovirus
+93678 Viruses; ssDNA viruses; Circoviridae; Anellovirus
+93934 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Galliformes; Phasianidae; Phasianinae; Coturnix
+94289 Eukaryota; Alveolata; Ciliophora; Spirotrichea; Stichotrichia; Stichotrichida; Oxytrichidae; Sterkiella
+94961 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Chiroptera; Microchiroptera; Mystacinidae; Mystacina
+95145 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Paracanthopterygii; Batrachoididae; Opsanus
+96939 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; Vitaceae; Vitis
+97005 Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Heteroderidae; Heteroderinae; Heterodera
+97393 Archaea; Euryarchaeota; Thermoplasmata; Thermoplasmatales; Ferroplasmaceae; Ferroplasma
+98038 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids II; Brassicales; Brassicaceae; Thellungiella
+99878 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Passeriformes; Sturnidae; Toxostoma
+99883 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Tetraodontiformes; Tetradontoidea; Tetraodontidae; Tetraodon
+100452 Eukaryota; Metazoa; Mollusca; Gastropoda; Pulmonata; Stylommatophora; Sigmurethra; Helicoidea; Hygromiidae; Candidula
+102803 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Cucujiformia; Phytophaga; Scolytidae; Ips
+103999 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; campanulids; Asterales; Campanulaceae; Codonopsis
+105358 Eukaryota; Metazoa; Echinodermata; Eleutherozoa; Echinozoa; Echinoidea; Euechinoidea; Diadematacea; Diadematoida; Diadematidae; Diadema
+105886 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; campanulids; Apiales; Araliaceae; Acanthopanax
+107832 Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Heterobasidiomycetes; Heterobasidiomycetidae; Ceratobasidiales; Ceratobasidiaceae; Thanatephorus
+107907 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Adephaga; Dytiscidae; Colymbetinae; Colymbetini; Meladema
+108098 Viruses; dsDNA viruses, no RNA stage; Adenoviridae; Mastadenovirus
+108607 Eukaryota; Pelobiontida; Mastigamoebidae; Mastigamoeba
+110365 Eukaryota; Alveolata; Apicomplexa; Gregarinia; Eugregarinida; Gregarinidae; Gregarina
+112525 Eukaryota; Metazoa; Mollusca; Gastropoda; Pulmonata; Basommatophora; Lymnaeoidea; Planorbidae; Biomphalaria
+113636 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Malpighiales; Salicaceae; Saliceae; Populus
+114524 Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
+114525 Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
+114526 Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
+117187 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; Nectriaceae; Gibberella
+118799 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Adephaga; Carabidae; Carabini; Carabina; Carabus; Carabus
+119072 Bacteria; Firmicutes; Clostridia; Thermoanaerobacteriales; Thermoanaerobacteriaceae; Thermoanaerobacter
+119219 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Ralstonia
+121225 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Phthiraptera; Anoplura; Pediculidae; Pediculus
+121759 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Onygenales; mitosporic Onygenales; Paracoccidioides
+123226 Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Scorpiones; Buthida; Buthoidea; Buthidae; Mesobuthus
+123792 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Sciuridae; Sciurinae; Tamias
+126740 Bacteria; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga
+126913 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Caryophyllales; Amaranthaceae; Suaeda
+128735 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Rosales; Rosaceae; Rosoideae; Rosa
+129883 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Cyprinidae; Telestes
+129951 Viruses; dsDNA viruses, no RNA stage; Adenoviridae; Mastadenovirus
+131310 Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Panagrolaimoidea; Strongyloididae; Parastrongyloides
+132711 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACCAD clade; Panicoideae; Andropogoneae; Sorghum
+134537 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Burkholderia
+135974 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Passeriformes; Furnariidae; Glyphorynchus
+136966 Viruses; ssDNA viruses; Circoviridae; Anellovirus
+137523 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Piciformes; Picidae; Dendrocopos
+138948 Viruses; ssRNA positive-strand viruses, no DNA stage; Picornaviridae; Enterovirus
+138949 Viruses; ssRNA positive-strand viruses, no DNA stage; Picornaviridae; Enterovirus
+138950 Viruses; ssRNA positive-strand viruses, no DNA stage; Picornaviridae; Enterovirus
+138953 Viruses; ssRNA positive-strand viruses, no DNA stage; Picornaviridae; Enterovirus
+140110 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; Nectriaceae; Nectria
+145262 Archaea; Euryarchaeota; Methanobacteria; Methanobacteriales; Methanobacteriaceae; Methanothermobacter
+148305 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariomycetes incertae sedis; Magnaporthaceae; Magnaporthe
+150234 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Adephaga; Cicindelidae; Cicindela; Cicindela
+153471 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Malpighiales; Salicaceae; Saliceae; Populus
+155892 Bacteria; Proteobacteria; Alphaproteobacteria; Caulobacterales; Caulobacteraceae; Caulobacter
+156889 Bacteria; Proteobacteria; Magnetococcus
+157791 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Vigna
+160621 Eukaryota; Alveolata; Dinophyceae; Gonyaulacales; Lingulodinium
+161934 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Caryophyllales; Amaranthaceae; Beta
+162425 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiales; Trichocomaceae; Emericella
+164405 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; Myrtales; Myrtaceae; Melaleuca
+172680 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Gruiformes; Otididae; Chlamydotis
+176275 Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; Clavicipitaceae; Cordyceps
+178872 Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Boletales; Sclerodermatineae; Pisolithaceae; Pisolithus
+180448 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Passeriformes; Motacillidae; Motacilla
+182803 Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Araneae; Araneomorphae; Entelegynae; Araneoidea; Araneidae; Araneus
+183855 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; Myrtales; Myrtaceae; Eucalyptus
+186039 Eukaryota; stramenopiles; Bacillariophyta; Bacillariophyceae; Bacillariophycidae; Bacillariales; Bacillariaceae; Fragilariopsis
+189293 Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Heteroderidae; Meloidogyninae; Meloidogyne
+189785 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Caryophyllales; Tamaricaceae; Tamarix
+194440 Viruses; Retroid viruses; Retroviridae; Deltaretrovirus
+194441 Viruses; Retroid viruses; Retroviridae; Deltaretrovirus
+197003 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Cucujiformia; Biphyllidae; Biphyllus
+197009 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Cucujiformia; Phytophaga; Anthribidae; Anthribinae; Platystomini; Platystomus
+197013 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Cucujiformia; Phytophaga; Curculionidae; Curculioninae; Curculionini; Curculio
+197043 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Hemiptera; Euhemiptera; Membracoidea; Cicadellidae; Cicadellinae; Homalodisca
+212795 Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Percoidei; Serranidae; Epinephelus
+213425 Eukaryota; Metazoa; Mollusca; Gastropoda; Orthogastropoda; Apogastropoda; Caenogastropoda; Sorbeoconcha; Hypsogastropoda; Neogastropoda; Muricoidea; Muricidae; Ocinebrellus
+216816 Bacteria; Actinobacteria; Actinobacteridae; Bifidobacteriales; Bifidobacteriaceae; Bifidobacterium
+219666 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Gentianales; Rubiaceae; Rubioideae; Spermacoceae; Hedyotis
+219667 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; asterids; lamiids; Gentianales; Rubiaceae; Rubioideae; Spermacoceae; Hedyotis
+219738 Eukaryota; Metazoa; Nematoda; Enoplea; Trichocephalida; Trichuridae; Trichuris
+221420 Eukaryota; Metazoa; Echinodermata; Eleutherozoa; Echinozoa; Holothuroidea; Aspidochirotacea; Aspidochirotida; Holothuriidae; Holothuria
+223153 Eukaryota; Alveolata; Ciliophora; Litostomatea; Trichostomatia; Vestibuliferida; Isotrichidae; Isotricha
+223852 Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Hemiptera; Sternorrhyncha; Aphidiformes; Aphidoidea; Aphididae; Aphidini; Toxoptera
+232323 Eukaryota; Metazoa; Tardigrada; Eutardigrada; Apochela; Hypsibiidae; Hypsibius
+241073 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; Vitaceae; Vitis
+245552 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Alstroemeriaceae; Alstroemeria
+246827 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; Vitaceae; Vitis
--- /dev/null
+PrintTemplateSet ::= {
+ {
+ name "StdSeqDesc" ,
+ format {
+ asn1 "Seqdesc" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Seqdesc.mol-type" ,
+ label "Molecule type" ,
+ prefix "\n" ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "Seqdesc.modif" ,
+ label "Modifiers" ,
+ prefix "\n" ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Seqdesc.modif.E" ,
+ form
+ enum {
+ } } } } } ,
+ {
+ asn1 "Seqdesc.method" ,
+ label "Method" ,
+ prefix "\n" ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "Seqdesc.name" ,
+ label "Name" ,
+ prefix "\n" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Seqdesc.title" ,
+ label "Title" ,
+ prefix "\n" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Seqdesc.org" ,
+ label "Organism" ,
+ prefix "\n" ,
+ form
+ use-template "StdOrgRef" } ,
+ {
+ asn1 "Seqdesc.comment" ,
+ label "Comment" ,
+ prefix "\n" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Seqdesc.num" ,
+ label "Numbering" ,
+ prefix "\n" ,
+ form
+ use-template "StdNumbering" } ,
+ {
+ asn1 "Seqdesc.maploc" ,
+ label "Map location" ,
+ prefix "\n" ,
+ form
+ use-template "StdDbtag" } ,
+ {
+ asn1 "Seqdesc.pir" ,
+ label "PIR block" ,
+ prefix "\n" ,
+ form
+ null NULL } ,
+ {
+ asn1 "Seqdesc.genbank" ,
+ label "GenBank block" ,
+ prefix "\n" ,
+ form
+ use-template "StdGBBlock" } ,
+ {
+ asn1 "Seqdesc.pub" ,
+ label "Citation" ,
+ prefix "\n" ,
+ form
+ use-template "StdPubdesc" } ,
+ {
+ asn1 "Seqdesc.region" ,
+ label "Region" ,
+ prefix "\n" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Seqdesc.user" ,
+ label "User Type" ,
+ prefix "\n" ,
+ form
+ use-template "StdUserObj" } ,
+ {
+ asn1 "Seqdesc.sp" ,
+ label "SWISS-PROT block" ,
+ prefix "\n" ,
+ form
+ null NULL } ,
+ {
+ asn1 "Seqdesc.dbxref" ,
+ label "Cross reference" ,
+ prefix "\n" ,
+ form
+ use-template "StdDbtag" } ,
+ {
+ asn1 "Seqdesc.embl" ,
+ label "EMBL block" ,
+ prefix "\n" ,
+ form
+ null NULL } ,
+ {
+ asn1 "Seqdesc.create-date" ,
+ label "Create date" ,
+ prefix "\n" ,
+ form
+ user {
+ printfunc "StdDatePrint" } } ,
+ {
+ asn1 "Seqdesc.update-date" ,
+ label "Update date" ,
+ prefix "\n" ,
+ form
+ user {
+ printfunc "StdDatePrint" } } ,
+ {
+ asn1 "Seqdesc.prf" ,
+ label "PRF block" ,
+ prefix "\n" ,
+ form
+ null NULL } ,
+ {
+ asn1 "Seqdesc.pdb" ,
+ label "PDB block" ,
+ prefix "\n" ,
+ form
+ null NULL } ,
+ {
+ asn1 "Seqdesc.het" ,
+ label "Heterogen" ,
+ prefix "\n" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Seqdesc.source" ,
+ label "Source" ,
+ prefix "\n" ,
+ form
+ null NULL } ,
+ {
+ asn1 "Seqdesc.molinfo" ,
+ label "Mol info" ,
+ prefix "\n" ,
+ form
+ null NULL } } } } } ,
+ {
+ name "StdReportSeqDesc" ,
+ format {
+ asn1 "Seqdesc" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Seqdesc.mol-type" ,
+ label "Molecule type" ,
+ prefix "\n" ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "Seqdesc.modif" ,
+ label "Modifiers" ,
+ prefix "\n" ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Seqdesc.modif.E" ,
+ form
+ enum {
+ } } } } } ,
+ {
+ asn1 "Seqdesc.method" ,
+ label "Method" ,
+ prefix "\n" ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "Seqdesc.name" ,
+ label "Name" ,
+ prefix "\n" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Seqdesc.title" ,
+ label "Title" ,
+ prefix "\n" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Seqdesc.org" ,
+ label "Organism" ,
+ prefix "\n" ,
+ form
+ use-template "StdOrgRef" } ,
+ {
+ asn1 "Seqdesc.comment" ,
+ label "Comment" ,
+ prefix "\n" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Seqdesc.num" ,
+ label "Numbering" ,
+ prefix "\n" ,
+ form
+ use-template "StdNumbering" } ,
+ {
+ asn1 "Seqdesc.maploc" ,
+ label "Map location" ,
+ prefix "\n" ,
+ form
+ use-template "StdDbtag" } ,
+ {
+ asn1 "Seqdesc.pir" ,
+ label "PIR block" ,
+ prefix "\n" ,
+ form
+ null NULL } ,
+ {
+ asn1 "Seqdesc.genbank" ,
+ prefix "\n" ,
+ form
+ use-template "StdReportGBBlock" } ,
+ {
+ asn1 "Seqdesc.pub" ,
+ label "Citation" ,
+ prefix "\n" ,
+ form
+ use-template "StdPubdesc" } ,
+ {
+ asn1 "Seqdesc.region" ,
+ label "Region" ,
+ prefix "\n" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Seqdesc.user" ,
+ label "User Type" ,
+ prefix "\n" ,
+ form
+ use-template "StdUserObj" } ,
+ {
+ asn1 "Seqdesc.sp" ,
+ label "SWISS-PROT block" ,
+ prefix "\n" ,
+ form
+ null NULL } ,
+ {
+ asn1 "Seqdesc.neighbors" ,
+ label "Neighbors" ,
+ prefix "\n" ,
+ form
+ null NULL } ,
+ {
+ asn1 "Seqdesc.embl" ,
+ label "EMBL block" ,
+ prefix "\n" ,
+ form
+ null NULL } ,
+ {
+ asn1 "Seqdesc.create-date" ,
+ label "Create date" ,
+ prefix "\n" ,
+ form
+ user {
+ printfunc "StdDatePrint" } } ,
+ {
+ asn1 "Seqdesc.update-date" ,
+ label "Update date" ,
+ prefix "\n" ,
+ form
+ user {
+ printfunc "StdDatePrint" } } ,
+ {
+ asn1 "Seqdesc.prf" ,
+ label "PRF block" ,
+ prefix "\n" ,
+ form
+ null NULL } ,
+ {
+ asn1 "Seqdesc.pdb" ,
+ label "PDB block" ,
+ prefix "\n" ,
+ form
+ null NULL } ,
+ {
+ asn1 "Seqdesc.het" ,
+ label "Heterogen" ,
+ prefix "\n" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Seqdesc.source" ,
+ label "Source" ,
+ prefix "\n" ,
+ form
+ null NULL } ,
+ {
+ asn1 "Seqdesc.molinfo" ,
+ label "Mol info" ,
+ prefix "\n" ,
+ form
+ null NULL } } } } } ,
+ {
+ name "StdSourceDesc" ,
+ format {
+ asn1 "Seqdesc" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Seqdesc.genbank" ,
+ prefix "\n" ,
+ form
+ use-template "StdSourceInGBBlock" } } } } } ,
+ {
+ name "StdTaxDesc" ,
+ format {
+ asn1 "Seqdesc" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Seqdesc.genbank" ,
+ prefix "\n" ,
+ form
+ use-template "StdTaxInGBBlock" } } } } } ,
+ {
+ name "StdDivDesc" ,
+ format {
+ asn1 "Seqdesc" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Seqdesc.genbank" ,
+ prefix "\n" ,
+ form
+ use-template "StdDivInGBBlock" } } } } } ,
+ {
+ name "StdSequenceId" ,
+ format {
+ asn1 "Seq-id" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Seq-id.gi" ,
+ label "gi|" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Seq-id.genbank" ,
+ form
+ use-template "ReportTextseqId" } ,
+ {
+ asn1 "Seq-id.local" ,
+ form
+ use-template "StdObjectId" } } } } } ,
+ {
+ name "StdPubSeqId" ,
+ format {
+ asn1 "Seq-id" ,
+ label "" ,
+ prefix "; " ,
+ form
+ block {
+ components {
+ {
+ asn1 "Seq-id.gi" ,
+ label "gi|" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Seq-id.local" ,
+ form
+ use-template "StdObjectId" } } } } } ,
+ {
+ name "StartingPubSeqId" ,
+ format {
+ asn1 "Seq-id" ,
+ label "Location:" ,
+ prefix "\t" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Seq-id.gi" ,
+ label "gi|" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Seq-id.local" ,
+ form
+ use-template "StdObjectId" } } } } } ,
+ {
+ name "StdObjectId" ,
+ format {
+ asn1 "Object-id" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Object-id.id" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Object-id.str" ,
+ form
+ text {
+ } } } } } } ,
+ {
+ name "StdTextseqId" ,
+ format {
+ asn1 "Textseq-id" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Textseq-id.name" ,
+ label "locus" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Textseq-id.accession" ,
+ label "accession" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Textseq-id.release" ,
+ label "release" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Textseq-id.version" ,
+ form
+ null NULL } ,
+ } } } } ,
+ {
+ name "ReportTextseqId" ,
+ format {
+ asn1 "Textseq-id" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Textseq-id.name" ,
+ label "locus" ,
+ prefix " " ,
+ suffix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Textseq-id.accession" ,
+ label "accession" ,
+ prefix " " ,
+ suffix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Textseq-id.release" ,
+ label "release" ,
+ prefix " " ,
+ suffix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Textseq-id.version" ,
+ form
+ null NULL } ,
+ } } } } ,
+ {
+ name "StdPDBseqId" ,
+ format {
+ asn1 "PDB-seq-id" ,
+ label "PDB Id: " ,
+ form
+ block {
+ components {
+ {
+ asn1 "PDB-seq-id.mol" ,
+ label "molecule" ,
+ prefix " " ,
+ suffix ", " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "PDB-seq-id.chain" ,
+ label "chain" ,
+ prefix " " ,
+ suffix ", " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "PDB-seq-id.rel" ,
+ label "release" ,
+ prefix " " ,
+ form
+ user {
+ printfunc "StdDatePrint" } } } } } } ,
+ {
+ name "StdEMBLseqId" ,
+ format {
+ asn1 "Textseq-id" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Textseq-id.name" ,
+ label "locus" ,
+ prefix " " ,
+ suffix ", " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Textseq-id.accession" ,
+ label "accession" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Textseq-id.release" ,
+ label "release" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Textseq-id.version" ,
+ form
+ null NULL } ,
+ } } } } ,
+ {
+ name "StdPIRseqId" ,
+ format {
+ asn1 "Textseq-id" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Textseq-id.name" ,
+ label "locus" ,
+ prefix " " ,
+ suffix "" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Textseq-id.accession" ,
+ label " accession" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ } } } } ,
+ {
+ name "StdPRFseqId" ,
+ format {
+ asn1 "Textseq-id" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Textseq-id.name" ,
+ label "locus" ,
+ prefix " " ,
+ suffix "" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Textseq-id.accession" ,
+ label " accession" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ } } } } ,
+ {
+ name "StdPDBseqId" ,
+ format {
+ asn1 "Textseq-id" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Textseq-id.name" ,
+ label "locus" ,
+ prefix " " ,
+ suffix "" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Textseq-id.accession" ,
+ label " accession" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ } } } } ,
+ {
+ name "StdSPseqId" ,
+ format {
+ asn1 "Textseq-id" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Textseq-id.name" ,
+ label "locus" ,
+ prefix " " ,
+ suffix "," ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Textseq-id.accession" ,
+ label " accession" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ } } } } ,
+ {
+ name "StdLocalId" ,
+ format {
+ asn1 "Object-id" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Object-id.id" ,
+ prefix " " ,
+ suffix "" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Object-id.str" ,
+ prefix " " ,
+ suffix "" ,
+ form
+ text {
+ } } } } } } ,
+ {
+ name "StdGPseqId" ,
+ format {
+ asn1 "Textseq-id" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Textseq-id.name" ,
+ label "locus" ,
+ prefix " " ,
+ suffix "," ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Textseq-id.accession" ,
+ label " accession" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ } } } } ,
+ {
+ name "StdIdPat" ,
+ format {
+ asn1 "Id-pat" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Id-pat.country" ,
+ suffix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Id-pat.id.number" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Id-pat.id.app-number" ,
+ prefix "Appl: " ,
+ form
+ text {
+ } } } } } } ,
+ {
+ name "StdPatentSeqId" ,
+ format {
+ asn1 "Patent-seq-id" ,
+ label "patent: " ,
+ form
+ block {
+ components {
+ {
+ asn1 "Patent-seq-id.seqid" ,
+ suffix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Patent-seq-id.cit" ,
+ prefix " " ,
+ form
+ use-template "StdIdPat" } } } } } ,
+ {
+ name "StdSeqFeatLocation" ,
+ format {
+ asn1 "Seq-feat.location" ,
+ label "Location" ,
+ prefix "\t" ,
+ form
+ user {
+ printfunc "StdSeqLocPrint" } } } ,
+ {
+ name "StdSeqFeatProduct" ,
+ format {
+ asn1 "Seq-feat.product" ,
+ label "Product" ,
+ prefix "\t" ,
+ form
+ user {
+ printfunc "StdSeqLocPrint" } } } ,
+ {
+ name "EntrySeqFeatData" ,
+ labelfrom "Seq-feat.data" ,
+ format {
+ asn1 "Seq-feat.data" ,
+ prefix "\t" ,
+ form
+ use-template "StdSeqFeatData" } } ,
+ {
+ name "StdSeqFeat" ,
+ labelfrom "Seq-feat.data" ,
+ format {
+ asn1 "Seq-feat" ,
+ prefix "\n" ,
+ suffix "\n" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Seq-feat.data" ,
+ form
+ use-template "StdSeqFeatData" } ,
+ {
+ asn1 "Seq-feat" ,
+ form
+ use-template "StdSeqFeatCommon" } ,
+ {
+ asn1 "Seq-feat.product" ,
+ label "Product" ,
+ prefix " " ,
+ form
+ user {
+ printfunc "StdSeqLocPrint" } } ,
+ {
+ asn1 "Seq-feat.location" ,
+ label "Location" ,
+ prefix " " ,
+ form
+ user {
+ printfunc "StdSeqLocPrint" } } ,
+ {
+ asn1 "Seq-feat.cit" ,
+ label "Citations" ,
+ prefix "\n" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Seq-feat.cit.pub.E" ,
+ form
+ use-template "StdPub" } } } } ,
+ {
+ asn1 "Seq-feat.xref" ,
+ label "Cross-reference" ,
+ prefix "\n" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Seq-feat.xref.E" ,
+ form
+ use-template "StdSeqFeatXref" } } } } } } } } ,
+ {
+ name "StdSeqFeatData" ,
+ format {
+ asn1 "SeqFeatData" ,
+ form
+ block {
+ components {
+ {
+ asn1 "SeqFeatData.gene" ,
+ label "Gene" ,
+ form
+ use-template "StdGeneRef" } ,
+ {
+ asn1 "SeqFeatData.org" ,
+ label "Organism" ,
+ form
+ use-template "StdOrgRef" } ,
+ {
+ asn1 "SeqFeatData.cdregion" ,
+ label "Coding Region" ,
+ form
+ use-template "StdCdRegion" } ,
+ {
+ asn1 "SeqFeatData.prot" ,
+ label "Protein" ,
+ form
+ use-template "StdProtRef" } ,
+ {
+ asn1 "SeqFeatData.rna" ,
+ label "RNA" ,
+ form
+ use-template "StdRNARef" } ,
+ {
+ asn1 "SeqFeatData.pub" ,
+ label "Citation" ,
+ form
+ use-template "StdPubdesc" } ,
+ {
+ asn1 "SeqFeatData.seq" ,
+ label "Sequence" ,
+ form
+ user {
+ printfunc "StdSeqLocPrint" } } ,
+ {
+ asn1 "SeqFeatData.imp.key" ,
+ label "Import" ,
+ form
+ use-template "StdImpFeat" } ,
+ {
+ asn1 "SeqFeatData.region" ,
+ label "Region" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "SeqFeatData.comment" ,
+ label "Comment" ,
+ form
+ null NULL } ,
+ {
+ asn1 "SeqFeatData.bond" ,
+ label "Bond" ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "SeqFeatData.site" ,
+ label "Site" ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "SeqFeatData.rsite" ,
+ label "Rest. Site" ,
+ form
+ use-template "StdRsiteRef" } ,
+ {
+ asn1 "SeqFeatData.user" ,
+ label "User Type" ,
+ form
+ use-template "StdUserObj" } ,
+ {
+ asn1 "SeqFeatData.txinit" ,
+ label "TxInit" ,
+ form
+ use-template "StdTxInit" } ,
+ {
+ asn1 "SeqFeatData.num" ,
+ label "Numbering" ,
+ form
+ use-template "StdNumbering" } ,
+ {
+ asn1 "SeqFeatData.psec-str" ,
+ label "Sec. Struct" ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "SeqFeatData.non-std-residue" ,
+ label "NonStd Residue" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "SeqFeatData.het" ,
+ label "Heterogen" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "SeqFeatData.biosrc" ,
+ label "BioSource" ,
+ form
+ null NULL } } } } } ,
+ {
+ name "StdGeneRef" ,
+ format {
+ asn1 "Gene-ref" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Gene-ref" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Gene-ref.locus" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Gene-ref.allele" ,
+ prefix " " ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "Gene-ref.desc" ,
+ prefix "[" ,
+ suffix "]" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Gene-ref.pseudo" ,
+ form
+ boolean {
+ true "This is a pseudogene." } } ,
+ {
+ asn1 "Gene-ref.syn" ,
+ label "Synonyms" ,
+ prefix " (" ,
+ suffix ")" ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Gene-ref.syn.E" ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "Gene-ref.maploc" ,
+ label "Map Location" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Gene-ref.db" ,
+ label "Cross Reference" ,
+ prefix " " ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Gene-ref.db.E" ,
+ prefix "(" ,
+ suffix ")" ,
+ form
+ use-template "StdDbtag" } } } } } } } } ,
+ {
+ name "StdUserObj" ,
+ format {
+ asn1 "User-object" ,
+ label "User-object" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "User-object.class" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "User-object.type" ,
+ form
+ use-template "StdObjectId" } } } } } ,
+ {
+ name "StartingPubFeatLocation" ,
+ format {
+ asn1 "Seq-feat.location" ,
+ label "Location:" ,
+ prefix "\t" ,
+ form
+ user {
+ printfunc "StdSeqLocPrint" } } } ,
+ {
+ name "StdPubFeatLocation" ,
+ format {
+ asn1 "Seq-feat.location" ,
+ label "" ,
+ prefix "; " ,
+ form
+ user {
+ printfunc "StdSeqLocPrint" } } } ,
+ {
+ name "StdPubOnFeat" ,
+ format {
+ asn1 "Pub" ,
+ label "Citation" ,
+ prefix "\n" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Pub" ,
+ form
+ use-template "StdPub" } } } } } ,
+ {
+ name "StdPub" ,
+ format {
+ asn1 "Pub" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Pub.gen" ,
+ form
+ use-template "StdCitGen" } ,
+ {
+ asn1 "Pub.sub" ,
+ form
+ use-template "StdCitSub" } ,
+ {
+ asn1 "Pub.medline" ,
+ form
+ use-template "StdMedlineEntry" } ,
+ {
+ asn1 "Pub.muid" ,
+ label "MEDLINE uid: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Pub.article" ,
+ form
+ use-template "StdCitArt" } ,
+ {
+ asn1 "Pub.journal" ,
+ form
+ use-template "StdCitJour" } ,
+ {
+ asn1 "Pub.book" ,
+ form
+ use-template "StdCitBook" } ,
+ {
+ asn1 "Pub.proc" ,
+ form
+ use-template "StdCitProc" } ,
+ {
+ asn1 "Pub.patent" ,
+ form
+ use-template "StdCitPat" } ,
+ {
+ asn1 "Pub.pat-id" ,
+ form
+ use-template "StdIdPat" } ,
+ {
+ asn1 "Pub.man" ,
+ form
+ use-template "StdCitLet" } ,
+ {
+ asn1 "Pub.equiv" ,
+ form
+ use-template "StdPubEquiv" } } } } } ,
+ {
+ name "StdCitGen" ,
+ format {
+ asn1 "Cit-gen" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Cit-gen.serial-number" ,
+ prefix "[" ,
+ suffix "]" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cit-gen.authors" ,
+ form
+ use-template "StdAuthList" } ,
+ {
+ asn1 "Cit-gen.date" ,
+ prefix "(" ,
+ suffix ")" ,
+ form
+ user {
+ printfunc "StdDatePrint" } } ,
+ {
+ asn1 "Cit-gen.title" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cit-gen.cit" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cit-gen" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Cit-gen.journal" ,
+ suffix ":" ,
+ form
+ use-template "StdTitle" } ,
+ {
+ asn1 "Cit-gen.issue" ,
+ suffix ";" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cit-gen.pages" ,
+ form
+ text {
+ } } } } } } } } } ,
+ {
+ name "StdCitSub" ,
+ format {
+ asn1 "Cit-sub" ,
+ prefix "Data Submission " ,
+ form
+ block {
+ components {
+ {
+ asn1 "Cit-sub.medium" ,
+ prefix "on " ,
+ suffix " " ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "Cit-sub.imp.date" ,
+ prefix "(" ,
+ suffix ")" ,
+ form
+ user {
+ printfunc "StdDatePrint" } } ,
+ {
+ asn1 "Cit-sub.authors" ,
+ prefix "\n" ,
+ form
+ use-template "StdAuthList" } } } } } ,
+ {
+ name "StdMedlineEntry" ,
+ format {
+ asn1 "Medline-entry" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Medline-entry" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Medline-entry.uid" ,
+ label "uid" ,
+ prefix ": " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Medline-entry.em" ,
+ label "entry month" ,
+ prefix ": " ,
+ form
+ user {
+ printfunc "StdDatePrint" } } } } } ,
+ {
+ asn1 "Medline-entry.cit" ,
+ form
+ use-template "StdCitArt" } ,
+ {
+ asn1 "Medline-entry.abstract" ,
+ label "abstract" ,
+ prefix ": " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Medline-entry.mesh" ,
+ label "Mesh Terms" ,
+ prefix "\n" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Medline-entry.mesh.E" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Medline-mesh.term" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Medline-mesh.mp" ,
+ form
+ boolean {
+ true " (Main Point)" } } ,
+ {
+ asn1 "Medline-mesh.qual" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Medline-mesh.qual.E" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Medline-qual.subh" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Medline-qual.mp" ,
+ form
+ boolean {
+ true " (Main Point)" } } } } } } } } } } } } } } ,
+ {
+ asn1 "Medline-entry.substance" ,
+ label "Substance" ,
+ prefix "\n" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Medline-entry.substance.E" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Medline-rn.name" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Medline-rn.type" ,
+ form
+ enum {
+ values {
+ "" ,
+ " CAS: " ,
+ "EC " } } } ,
+ {
+ asn1 "Medline-rn.cit" ,
+ form
+ text {
+ } } } } } } } } ,
+ {
+ asn1 "Medline-entry.xref" ,
+ label "Cross Reference" ,
+ prefix "\n" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Medline-entry.xref.E" ,
+ form
+ block {
+ separator ": " ,
+ components {
+ {
+ asn1 "Medline-si.type" ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "Medline-si.cit" ,
+ form
+ text {
+ } } } } } } } } ,
+ {
+ asn1 "Medline-entry.gene" ,
+ label "Possible Gene Symbols" ,
+ prefix ": " ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Medline-entry.gene.E" ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "Medline-entry.idnum" ,
+ label "Support" ,
+ prefix ": " ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Medline-entry.idnum.E" ,
+ form
+ text {
+ } } } } } } } } } ,
+ {
+ name "StdCitArt" ,
+ format {
+ asn1 "Cit-art" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Cit-art.title" ,
+ form
+ use-template "StdTitle" } ,
+ {
+ asn1 "Cit-art.authors" ,
+ form
+ use-template "StdAuthList" } ,
+ {
+ asn1 "Cit-art.from.journal" ,
+ form
+ use-template "StdCitJour" } ,
+ {
+ asn1 "Cit-art.from.book" ,
+ prefix "(in) " ,
+ form
+ use-template "StdCitBook" } ,
+ {
+ asn1 "Cit-art.from.proc" ,
+ prefix "(in) " ,
+ form
+ use-template "StdCitProc" } } } } } ,
+ {
+ name "StdCitJour" ,
+ format {
+ asn1 "Cit-jour" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Cit-jour.title" ,
+ form
+ use-template "StdTitle" } ,
+ {
+ asn1 "Cit-jour.imp" ,
+ form
+ use-template "StdImprint" } } } } } ,
+ {
+ name "StdCitBook" ,
+ format {
+ asn1 "Cit-book" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Cit-book.title" ,
+ form
+ use-template "StdTitle" } ,
+ {
+ asn1 "Cit-book.coll" ,
+ prefix "Collection: " ,
+ form
+ use-template "StdTitle" } ,
+ {
+ asn1 "Cit-book.authors" ,
+ form
+ use-template "StdAuthList" } ,
+ {
+ asn1 "Cit-book.imp" ,
+ form
+ use-template "StdImprint" } } } } } ,
+ {
+ name "StdCitProc" ,
+ format {
+ asn1 "Cit-proc" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Cit-proc.book" ,
+ form
+ use-template "StdCitBook" } ,
+ {
+ asn1 "Cit-proc.meet" ,
+ label "Meeting " ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Meeting.number" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Meeting.date" ,
+ form
+ user {
+ printfunc "StdDatePrint" } } ,
+ {
+ asn1 "Meeting.place" ,
+ form
+ use-template "StdAffil" } } } } } } } } ,
+ {
+ name "StdCitPat" ,
+ format {
+ asn1 "Cit-pat" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Cit-pat.title" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cit-pat.authors" ,
+ form
+ use-template "StdAuthList" } ,
+ {
+ asn1 "Cit-pat" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Cit-pat.country" ,
+ suffix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cit-pat.doc-type" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cit-pat.number" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cit-pat.date-issue" ,
+ prefix " (" ,
+ suffix ")" ,
+ form
+ user {
+ printfunc "StdDatePrint" } } ,
+ {
+ asn1 "Cit-pat.app-number" ,
+ prefix " Appl: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cit-pat.app-date" ,
+ prefix " (" ,
+ suffix ")" ,
+ form
+ user {
+ printfunc "StdDatePrint" } } } } } } } } } ,
+ {
+ name "StdIdPat" ,
+ format {
+ asn1 "Id-pat" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Id-pat.country" ,
+ suffix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Id-pat.id.number" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Id-pat.id.app-number" ,
+ prefix "Appl: " ,
+ form
+ text {
+ } } } } } } ,
+ {
+ name "StdCitLet" ,
+ format {
+ asn1 "Cit-let" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Cit-let.type" ,
+ prefix "[" ,
+ suffix "]" ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "Cit-let.man-id" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cit-let.cit" ,
+ form
+ use-template "StdCitBook" } } } } } ,
+ {
+ name "StdPubEquiv" ,
+ format {
+ asn1 "Pub-equiv" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Pub-equiv.E" ,
+ form
+ use-template "StdPub" } } } } } ,
+ {
+ name "StdTitle" ,
+ format {
+ asn1 "Title" ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Title.E.trans" ,
+ prefix "[" ,
+ suffix "]" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Title.E.name" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Title.E.tsub" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Title.E.abr" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Title.E.iso-jta" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Title.E.ml-jta" ,
+ label "MEDLINE" ,
+ prefix ": " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Title.E.jta" ,
+ label "jta" ,
+ prefix ": " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Title.E.issn" ,
+ label "ISSN" ,
+ prefix ": " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Title.E.coden" ,
+ label "CODEN" ,
+ prefix ": " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Title.E.isbn" ,
+ label "ISBN" ,
+ prefix ": " ,
+ form
+ text {
+ } } } } } } ,
+ {
+ name "StdAuthList" ,
+ format {
+ asn1 "Auth-list" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Auth-list" ,
+ form
+ user {
+ printfunc "StdAuthListNamesPrint" } } ,
+ {
+ asn1 "Auth-list.affil" ,
+ form
+ use-template "StdAffil" } } } } } ,
+ {
+ name "StdAffil" ,
+ format {
+ asn1 "Affil" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Affil.str" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Affil.std.affil" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Affil.std.div" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Affil.std.street" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Affil.std" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Affil.std.city" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Affil.std.sub" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Affil.std.country" ,
+ form
+ text {
+ } } } } } } } } } ,
+ {
+ name "StdImprint" ,
+ format {
+ asn1 "Imprint" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Imprint.date" ,
+ prefix "(" ,
+ suffix ") " ,
+ form
+ user {
+ printfunc "StdDatePrint" } } ,
+ {
+ asn1 "Imprint.volume" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Imprint.issue" ,
+ prefix " (" ,
+ suffix ")" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Imprint.section" ,
+ prefix " (" ,
+ suffix ")" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Imprint.part-sup" ,
+ prefix " (" ,
+ suffix ")" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Imprint.pages" ,
+ prefix ": " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Imprint.prepub" ,
+ prefix " (" ,
+ suffix ")" ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "Imprint.pub" ,
+ label "\nPublisher: " ,
+ form
+ use-template "StdAffil" } ,
+ {
+ asn1 "Imprint.cprt" ,
+ label " Copyright: " ,
+ form
+ user {
+ printfunc "StdDatePrint" } } } } } } ,
+ {
+ name "StdSeqFeatXref" ,
+ format {
+ asn1 "SeqFeatXref" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "SeqFeatXref.id" ,
+ label "Id=" ,
+ form
+ use-template "StdFeatId" } ,
+ {
+ asn1 "SeqFeatXref.data" ,
+ form
+ use-template "StdSeqFeatData" } } } } } ,
+ {
+ name "StdOrgRef" ,
+ format {
+ asn1 "Org-ref" ,
+ label "Org-ref" ,
+ prefix "\n" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Org-ref" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Org-ref.taxname" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Org-ref.common" ,
+ prefix "(" ,
+ suffix ")" ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "Org-ref.mod" ,
+ label "Modifiers" ,
+ prefix " (" ,
+ suffix ")" ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Org-ref.mod.E" ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "Org-ref.db" ,
+ label "Cross Reference" ,
+ prefix " " ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Org-ref.db.E" ,
+ prefix "(" ,
+ suffix ")" ,
+ form
+ use-template "StdDbtag" } } } } ,
+ {
+ asn1 "Org-ref.syn" ,
+ label "Synonyms" ,
+ prefix " (" ,
+ suffix ")" ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Org-ref.syn.E" ,
+ form
+ text {
+ } } } } } } } } } ,
+ {
+ name "StdCdRegion" ,
+ format {
+ asn1 "Cdregion" ,
+ label "Cdregion" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Cdregion.orf" ,
+ form
+ boolean {
+ true "Uncharacterized Open Reading Frame" } } ,
+ {
+ asn1 "Cdregion.frame" ,
+ label "Reading Frame = " ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "Cdregion.code" ,
+ label "Genetic Code: " ,
+ suffix ";" ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Genetic-code.E.name" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Genetic-code.E.id" ,
+ label "id= " ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "Cdregion.conflict" ,
+ form
+ boolean {
+ true "Translation conflicts with protein sequence" } } ,
+ {
+ asn1 "Cdregion.stops" ,
+ prefix "Translation contains " ,
+ suffix " stop codons" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cdregion.gaps" ,
+ prefix "Translation contains " ,
+ suffix " gaps when aligned to protein" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cdregion.mismatch" ,
+ prefix "Translation contains " ,
+ suffix " mismatches when aligned to protein" ,
+ form
+ text {
+ } } } } } } ,
+ {
+ name "StdProtRef" ,
+ format {
+ asn1 "Prot-ref" ,
+ label "Prot-ref" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Prot-ref.name" ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Prot-ref.name.E" ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "Prot-ref.desc" ,
+ prefix "[" ,
+ suffix "]" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Prot-ref.ec" ,
+ label "ec" ,
+ prefix ": " ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Prot-ref.ec.E" ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "Prot-ref.activity" ,
+ label "activity" ,
+ prefix ": " ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Prot-ref.activity.E" ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "Prot-ref.db" ,
+ form
+ use-template "StdDbtag" } } } } } ,
+ {
+ name "StdRNARef" ,
+ format {
+ asn1 "RNA-ref" ,
+ label "RNA-ref" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "RNA-ref.type" ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "RNA-ref.pseudo" ,
+ form
+ boolean {
+ true "This is an RNA pseudogene." } } ,
+ {
+ asn1 "RNA-ref.ext.name" ,
+ form
+ text {
+ } } } } } } ,
+ {
+ name "StdPubdesc" ,
+ format {
+ asn1 "Pubdesc" ,
+ label "Pubdesc" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Pubdesc.pub" ,
+ form
+ use-template "StdPubEquiv" } ,
+ {
+ asn1 "Pubdesc" ,
+ prefix "In this article:\n" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Pubdesc.name" ,
+ label "name=" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Pubdesc.fig" ,
+ label "figure=" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Pubdesc.poly-a" ,
+ form
+ boolean {
+ true "poly(A) shown" } } ,
+ {
+ asn1 "Pubdesc.maploc" ,
+ label "map location=" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Pubdesc.num" ,
+ form
+ use-template "StdNumbering" } ,
+ {
+ asn1 "Pubdesc.numexc" ,
+ form
+ boolean {
+ true "numbering inconsistent" } } } } } ,
+ {
+ asn1 "Pubdesc.comment" ,
+ form
+ text {
+ } } } } } } ,
+ {
+ name "StdImpFeat" ,
+ format {
+ asn1 "Imp-feat.key" ,
+ label "Imp-feat" ,
+ form
+ text {
+ } } } ,
+ {
+ name "StdRsiteRef" ,
+ format {
+ asn1 "Rsite-ref" ,
+ label "Rsite-ref" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Rsite-ref.str" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Rsite-ref.std" ,
+ form
+ use-template "StdDbtag" } } } } } ,
+ {
+ name "StdTxInit" ,
+ format {
+ asn1 "Txinit" ,
+ label "TxInit" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Txinit.name" ,
+ form
+ text {
+ } } } } } } ,
+ {
+ name "StdNumbering" ,
+ format {
+ asn1 "Numbering" ,
+ label "Numbering" ,
+ form
+ null NULL } } ,
+ {
+ name "StdGBBlock" ,
+ format {
+ asn1 "GB-block" ,
+ label "GenBank-block" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "GB-block.extra-accessions" ,
+ label "Extra accessions" ,
+ prefix " (" ,
+ suffix ")" ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "GB-block.extra-accessions.E" ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "GB-block.keywords" ,
+ label "Keywords" ,
+ prefix " (" ,
+ suffix ")" ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "GB-block.keywords.E" ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "GB-block.source" ,
+ label "Source: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "GB-block.origin" ,
+ label "Origin: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "GB-block.div" ,
+ label "Division: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "GB-block.taxonomy" ,
+ label "Taxonomy: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "GB-block.date" ,
+ label "Date: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "GB-block.entry-date" ,
+ label "Entry date: " ,
+ form
+ user {
+ printfunc "StdDatePrint" } } } } } } ,
+ {
+ name "StdReportGBBlock" ,
+ format {
+ asn1 "GB-block" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "GB-block.extra-accessions" ,
+ label "Extra accessions" ,
+ prefix " (" ,
+ suffix ")" ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "GB-block.extra-accessions.E" ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "GB-block.keywords" ,
+ label "Keywords" ,
+ prefix " (" ,
+ suffix ")" ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "GB-block.keywords.E" ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "GB-block.origin" ,
+ label "Origin: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "GB-block.date" ,
+ label "Date: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "GB-block.entry-date" ,
+ label "Entry date: " ,
+ form
+ user {
+ printfunc "StdDatePrint" } } } } } } ,
+ {
+ name "StdSourceInGBBlock" ,
+ format {
+ asn1 "GB-block" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "GB-block.source" ,
+ label "Source: " ,
+ form
+ text {
+ } } } } } } ,
+ {
+ name "StdDivInGBBlock" ,
+ format {
+ asn1 "GB-block" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "GB-block.div" ,
+ label "Division: " ,
+ form
+ text {
+ } } } } } } ,
+ {
+ name "StdTaxInGBBlock" ,
+ format {
+ asn1 "GB-block" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "GB-block.taxonomy" ,
+ label "Taxonomy: " ,
+ form
+ text {
+ } } } } } } ,
+ {
+ name "StdFeatId" ,
+ format {
+ asn1 "Feat-id" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Feat-id.gibb" ,
+ label "GenInfo Backbone: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Feat-id.giim.id" ,
+ label "GenInfo Import Id: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Feat-id.local" ,
+ label "Local: " ,
+ form
+ use-template "StdObjectId" } ,
+ {
+ asn1 "Feat-id.general" ,
+ form
+ use-template "StdDbtag" } } } } } ,
+ {
+ name "StdSeqFeatCommon" ,
+ format {
+ asn1 "Seq-feat" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Seq-feat.id" ,
+ label "Id=" ,
+ form
+ use-template "StdFeatId" } ,
+ {
+ asn1 "Seq-feat.title" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Seq-feat" ,
+ suffix ";" ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Seq-feat.partial" ,
+ form
+ boolean {
+ true "Partial" } } ,
+ {
+ asn1 "Seq-feat.except" ,
+ form
+ boolean {
+ true "Biological Exception" } } ,
+ {
+ asn1 "Seq-feat.exp-ev" ,
+ label "Evidence" ,
+ prefix " is " ,
+ form
+ enum {
+ } } } } } ,
+ {
+ asn1 "Seq-feat.comment" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Seq-feat.ext" ,
+ form
+ use-template "StdUserObj" } ,
+ {
+ asn1 "Seq-feat.qual" ,
+ label "Qualifiers" ,
+ prefix "\n" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Seq-feat.qual.E" ,
+ prefix "/" ,
+ form
+ block {
+ separator "= " ,
+ components {
+ {
+ asn1 "Gb-qual.qual" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Gb-qual.val" ,
+ form
+ text {
+ } } } } } } } } } } } } ,
+ {
+ name "StdDbtag" ,
+ format {
+ asn1 "Dbtag" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Dbtag.db" ,
+ suffix ": " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Dbtag.tag" ,
+ form
+ use-template "StdObjectId" } } } } } ,
+ {
+ name "StdObjectId" ,
+ format {
+ asn1 "Object-id" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Object-id.id" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Object-id.str" ,
+ form
+ text {
+ } } } } } } }
--- /dev/null
+PrintTemplateSet ::= {
+ {
+ name "StdSeqDesc" ,
+ format {
+ asn1 "Seqdesc" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Seqdesc.mol-type" ,
+ label "Molecule type" ,
+ prefix "\n" ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "Seqdesc.modif" ,
+ label "Modifiers" ,
+ prefix "\n" ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Seqdesc.modif.E" ,
+ form
+ enum {
+ } } } } } ,
+ {
+ asn1 "Seqdesc.method" ,
+ label "Method" ,
+ prefix "\n" ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "Seqdesc.name" ,
+ label "Name" ,
+ prefix "\n" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Seqdesc.title" ,
+ label "Title" ,
+ prefix "\n" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Seqdesc.org" ,
+ label "Organism" ,
+ prefix "\n" ,
+ form
+ use-template "StdOrgRef" } ,
+ {
+ asn1 "Seqdesc.comment" ,
+ label "Comment" ,
+ prefix "\n" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Seqdesc.num" ,
+ label "Numbering" ,
+ prefix "\n" ,
+ form
+ use-template "StdNumbering" } ,
+ {
+ asn1 "Seqdesc.maploc" ,
+ label "Map location" ,
+ prefix "\n" ,
+ form
+ use-template "StdDbtag" } ,
+ {
+ asn1 "Seqdesc.pir" ,
+ label "PIR block" ,
+ prefix "\n" ,
+ form
+ null NULL } ,
+ {
+ asn1 "Seqdesc.genbank" ,
+ label "GenBank block" ,
+ prefix "\n" ,
+ form
+ use-template "StdGBBlock" } ,
+ {
+ asn1 "Seqdesc.pub" ,
+ label "Citation" ,
+ prefix "\n" ,
+ form
+ use-template "StdPubdesc" } ,
+ {
+ asn1 "Seqdesc.region" ,
+ label "Region" ,
+ prefix "\n" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Seqdesc.user" ,
+ label "User Type" ,
+ prefix "\n" ,
+ form
+ use-template "StdUserObj" } ,
+ {
+ asn1 "Seqdesc.sp" ,
+ label "SWISS-PROT block" ,
+ prefix "\n" ,
+ form
+ null NULL } ,
+ {
+ asn1 "Seqdesc.dbxref" ,
+ label "Cross reference" ,
+ prefix "\n" ,
+ form
+ use-template "StdDbtag" } ,
+ {
+ asn1 "Seqdesc.embl" ,
+ label "EMBL block" ,
+ prefix "\n" ,
+ form
+ null NULL } ,
+ {
+ asn1 "Seqdesc.create-date" ,
+ label "Create date" ,
+ prefix "\n" ,
+ form
+ user {
+ printfunc "StdDatePrint" } } ,
+ {
+ asn1 "Seqdesc.update-date" ,
+ label "Update date" ,
+ prefix "\n" ,
+ form
+ user {
+ printfunc "StdDatePrint" } } ,
+ {
+ asn1 "Seqdesc.prf" ,
+ label "PRF block" ,
+ prefix "\n" ,
+ form
+ null NULL } ,
+ {
+ asn1 "Seqdesc.pdb" ,
+ label "PDB block" ,
+ prefix "\n" ,
+ form
+ null NULL } ,
+ {
+ asn1 "Seqdesc.het" ,
+ label "Heterogen" ,
+ prefix "\n" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Seqdesc.source" ,
+ label "Biological Source" ,
+ prefix "\n" ,
+ form
+ use-template "StdBioSource" } ,
+ {
+ asn1 "Seqdesc.molinfo" ,
+ label "Molecule Information" ,
+ prefix "\n" ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "MolInfo.biomol" ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "MolInfo.tech" ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "MolInfo.completeness" ,
+ form
+ enum {
+ } } } } } } } } } ,
+ {
+ name "StdSeqFeatLocation" ,
+ format {
+ asn1 "Seq-feat.location" ,
+ label "Location" ,
+ prefix "\t" ,
+ form
+ user {
+ printfunc "StdSeqLocPrint" } } } ,
+ {
+ name "StdSeqFeatProduct" ,
+ format {
+ asn1 "Seq-feat.product" ,
+ label "Product" ,
+ prefix "\t" ,
+ form
+ user {
+ printfunc "StdSeqLocPrint" } } } ,
+ {
+ name "EntrySeqFeatData" ,
+ labelfrom "Seq-feat.data" ,
+ format {
+ asn1 "Seq-feat.data" ,
+ prefix "\t" ,
+ form
+ use-template "StdSeqFeatData" } } ,
+ {
+ name "StdSeqFeat" ,
+ labelfrom "Seq-feat.data" ,
+ format {
+ asn1 "Seq-feat" ,
+ prefix "\n" ,
+ suffix "\n" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Seq-feat.data" ,
+ form
+ use-template "StdSeqFeatData" } ,
+ {
+ asn1 "Seq-feat" ,
+ form
+ use-template "StdSeqFeatCommon" } ,
+ {
+ asn1 "Seq-feat.product" ,
+ label "Product" ,
+ prefix " " ,
+ form
+ user {
+ printfunc "StdSeqLocPrint" } } ,
+ {
+ asn1 "Seq-feat.location" ,
+ label "Location" ,
+ prefix " " ,
+ form
+ user {
+ printfunc "StdSeqLocPrint" } } ,
+ {
+ asn1 "Seq-feat.cit" ,
+ label "Citations" ,
+ prefix "\n" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Seq-feat.cit.pub.E" ,
+ form
+ use-template "StdPub" } } } } ,
+ {
+ asn1 "Seq-feat.xref" ,
+ label "Cross-reference" ,
+ prefix "\n" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Seq-feat.xref.E" ,
+ form
+ use-template "StdSeqFeatXref" } } } } } } } } ,
+ {
+ name "StdSeqFeatData" ,
+ format {
+ asn1 "SeqFeatData" ,
+ form
+ block {
+ components {
+ {
+ asn1 "SeqFeatData.gene" ,
+ label "Gene" ,
+ form
+ use-template "StdGeneRef" } ,
+ {
+ asn1 "SeqFeatData.org" ,
+ label "Organism" ,
+ form
+ use-template "StdOrgRef" } ,
+ {
+ asn1 "SeqFeatData.cdregion" ,
+ label "Coding Region" ,
+ form
+ use-template "StdCdRegion" } ,
+ {
+ asn1 "SeqFeatData.prot" ,
+ label "Protein" ,
+ form
+ use-template "StdProtRef" } ,
+ {
+ asn1 "SeqFeatData.rna" ,
+ label "RNA" ,
+ form
+ use-template "StdRNARef" } ,
+ {
+ asn1 "SeqFeatData.pub" ,
+ label "Citation" ,
+ form
+ use-template "StdPubdesc" } ,
+ {
+ asn1 "SeqFeatData.seq" ,
+ label "Sequence" ,
+ form
+ user {
+ printfunc "StdSeqLocPrint" } } ,
+ {
+ asn1 "SeqFeatData.imp.key" ,
+ label "Import" ,
+ form
+ use-template "StdImpFeat" } ,
+ {
+ asn1 "SeqFeatData.region" ,
+ label "Region" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "SeqFeatData.comment" ,
+ label "Comment" ,
+ form
+ null NULL } ,
+ {
+ asn1 "SeqFeatData.bond" ,
+ label "Bond" ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "SeqFeatData.site" ,
+ label "Site" ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "SeqFeatData.rsite" ,
+ label "Rest. Site" ,
+ form
+ use-template "StdRsiteRef" } ,
+ {
+ asn1 "SeqFeatData.user" ,
+ label "User Type" ,
+ form
+ use-template "StdUserObj" } ,
+ {
+ asn1 "SeqFeatData.txinit" ,
+ label "TxInit" ,
+ form
+ use-template "StdTxInit" } ,
+ {
+ asn1 "SeqFeatData.num" ,
+ label "Numbering" ,
+ form
+ use-template "StdNumbering" } ,
+ {
+ asn1 "SeqFeatData.psec-str" ,
+ label "Sec. Struct" ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "SeqFeatData.non-std-residue" ,
+ label "NonStd Residue" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "SeqFeatData.het" ,
+ label "Heterogen" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "SeqFeatData.biosrc" ,
+ label "Biological Source" ,
+ prefix "\n" ,
+ form
+ use-template "StdBioSource" } } } } } ,
+ {
+ name "StdGeneRef" ,
+ format {
+ asn1 "Gene-ref" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Gene-ref" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Gene-ref.locus" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Gene-ref.allele" ,
+ prefix " " ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "Gene-ref.desc" ,
+ prefix "[" ,
+ suffix "]" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Gene-ref.pseudo" ,
+ form
+ boolean {
+ true "This is a pseudogene." } } ,
+ {
+ asn1 "Gene-ref.syn" ,
+ label "Synonyms" ,
+ prefix " (" ,
+ suffix ")" ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Gene-ref.syn.E" ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "Gene-ref.maploc" ,
+ label "Map Location" ,
+ prefix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Gene-ref.db" ,
+ label "Cross Reference" ,
+ prefix " " ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Gene-ref.db.E" ,
+ prefix "(" ,
+ suffix ")" ,
+ form
+ use-template "StdDbtag" } } } } } } } } ,
+ {
+ name "StdUserObj" ,
+ format {
+ asn1 "User-object" ,
+ label "User-object" ,
+ prefix "\n" ,
+ form
+ block {
+ separator ": " ,
+ components {
+ {
+ asn1 "User-object.class" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "User-object.type" ,
+ form
+ use-template "StdObjectId" } } } } } ,
+ {
+ name "StdPubOnFeat" ,
+ format {
+ asn1 "Pub" ,
+ label "Citation" ,
+ prefix "\n" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Pub" ,
+ form
+ use-template "StdPub" } } } } } ,
+ {
+ name "StdPub" ,
+ format {
+ asn1 "Pub" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Pub.gen" ,
+ form
+ use-template "StdCitGen" } ,
+ {
+ asn1 "Pub.sub" ,
+ form
+ use-template "StdCitSub" } ,
+ {
+ asn1 "Pub.medline" ,
+ form
+ use-template "StdMedlineEntry" } ,
+ {
+ asn1 "Pub.muid" ,
+ label "MEDLINE uid: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Pub.pmid" ,
+ label "PubMed id: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Pub.article" ,
+ form
+ use-template "StdCitArt" } ,
+ {
+ asn1 "Pub.journal" ,
+ form
+ use-template "StdCitJour" } ,
+ {
+ asn1 "Pub.book" ,
+ form
+ use-template "StdCitBook" } ,
+ {
+ asn1 "Pub.proc" ,
+ form
+ use-template "StdCitProc" } ,
+ {
+ asn1 "Pub.patent" ,
+ form
+ use-template "StdCitPat" } ,
+ {
+ asn1 "Pub.pat-id" ,
+ form
+ use-template "StdIdPat" } ,
+ {
+ asn1 "Pub.man" ,
+ form
+ use-template "StdCitLet" } ,
+ {
+ asn1 "Pub.equiv" ,
+ form
+ use-template "StdPubEquiv" } } } } } ,
+ {
+ name "StdCitGen" ,
+ format {
+ asn1 "Cit-gen" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Cit-gen.serial-number" ,
+ prefix "[" ,
+ suffix "]" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cit-gen.authors" ,
+ form
+ use-template "StdAuthList" } ,
+ {
+ asn1 "Cit-gen.date" ,
+ prefix "(" ,
+ suffix ")" ,
+ form
+ user {
+ printfunc "StdDatePrint" } } ,
+ {
+ asn1 "Cit-gen.title" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cit-gen.cit" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cit-gen" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Cit-gen.journal" ,
+ suffix ":" ,
+ form
+ use-template "StdTitle" } ,
+ {
+ asn1 "Cit-gen.issue" ,
+ suffix ";" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cit-gen.pages" ,
+ form
+ text {
+ } } } } } } } } } ,
+ {
+ name "StdCitSub" ,
+ format {
+ asn1 "Cit-sub" ,
+ prefix "Data Submission " ,
+ form
+ block {
+ components {
+ {
+ asn1 "Cit-sub.medium" ,
+ prefix "on " ,
+ suffix " " ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "Cit-sub.imp.date" ,
+ prefix "(" ,
+ suffix ")" ,
+ form
+ user {
+ printfunc "StdDatePrint" } } ,
+ {
+ asn1 "Cit-sub.authors" ,
+ prefix "\n" ,
+ form
+ use-template "StdAuthList" } } } } } ,
+ {
+ name "StdMedlineEntry" ,
+ format {
+ asn1 "Medline-entry" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Medline-entry" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Medline-entry.uid" ,
+ label "uid" ,
+ prefix ": " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Medline-entry.em" ,
+ label "entry month" ,
+ prefix ": " ,
+ form
+ user {
+ printfunc "StdDatePrint" } } } } } ,
+ {
+ asn1 "Medline-entry.cit" ,
+ form
+ use-template "StdCitArt" } ,
+ {
+ asn1 "Medline-entry.abstract" ,
+ label "abstract" ,
+ prefix ": " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Medline-entry.mesh" ,
+ label "Mesh Terms" ,
+ prefix "\n" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Medline-entry.mesh.E" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Medline-mesh.term" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Medline-mesh.mp" ,
+ form
+ boolean {
+ true " (Main Point)" } } ,
+ {
+ asn1 "Medline-mesh.qual" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Medline-mesh.qual.E" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Medline-qual.subh" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Medline-qual.mp" ,
+ form
+ boolean {
+ true " (Main Point)" } } } } } } } } } } } } } } ,
+ {
+ asn1 "Medline-entry.substance" ,
+ label "Substance" ,
+ prefix "\n" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Medline-entry.substance.E" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Medline-rn.name" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Medline-rn.type" ,
+ form
+ enum {
+ values {
+ "" ,
+ " CAS: " ,
+ "EC " } } } ,
+ {
+ asn1 "Medline-rn.cit" ,
+ form
+ text {
+ } } } } } } } } ,
+ {
+ asn1 "Medline-entry.xref" ,
+ label "Cross Reference" ,
+ prefix "\n" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Medline-entry.xref.E" ,
+ form
+ block {
+ separator ": " ,
+ components {
+ {
+ asn1 "Medline-si.type" ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "Medline-si.cit" ,
+ form
+ text {
+ } } } } } } } } ,
+ {
+ asn1 "Medline-entry.gene" ,
+ label "Possible Gene Symbols" ,
+ prefix ": " ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Medline-entry.gene.E" ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "Medline-entry.idnum" ,
+ label "Support" ,
+ prefix ": " ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Medline-entry.idnum.E" ,
+ form
+ text {
+ } } } } } } } } } ,
+ {
+ name "StdCitArt" ,
+ format {
+ asn1 "Cit-art" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Cit-art.title" ,
+ form
+ use-template "StdTitle" } ,
+ {
+ asn1 "Cit-art.authors" ,
+ form
+ use-template "StdAuthList" } ,
+ {
+ asn1 "Cit-art.from.journal" ,
+ form
+ use-template "StdCitJour" } ,
+ {
+ asn1 "Cit-art.from.book" ,
+ prefix "(in) " ,
+ form
+ use-template "StdCitBook" } ,
+ {
+ asn1 "Cit-art.from.proc" ,
+ prefix "(in) " ,
+ form
+ use-template "StdCitProc" } } } } } ,
+ {
+ name "StdCitJour" ,
+ format {
+ asn1 "Cit-jour" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Cit-jour.title" ,
+ form
+ use-template "StdTitle" } ,
+ {
+ asn1 "Cit-jour.imp" ,
+ form
+ use-template "StdImprint" } } } } } ,
+ {
+ name "StdCitBook" ,
+ format {
+ asn1 "Cit-book" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Cit-book.title" ,
+ form
+ use-template "StdTitle" } ,
+ {
+ asn1 "Cit-book.coll" ,
+ prefix "Collection: " ,
+ form
+ use-template "StdTitle" } ,
+ {
+ asn1 "Cit-book.authors" ,
+ form
+ use-template "StdAuthList" } ,
+ {
+ asn1 "Cit-book.imp" ,
+ form
+ use-template "StdImprint" } } } } } ,
+ {
+ name "StdCitProc" ,
+ format {
+ asn1 "Cit-proc" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Cit-proc.book" ,
+ form
+ use-template "StdCitBook" } ,
+ {
+ asn1 "Cit-proc.meet" ,
+ label "Meeting " ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Meeting.number" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Meeting.date" ,
+ form
+ user {
+ printfunc "StdDatePrint" } } ,
+ {
+ asn1 "Meeting.place" ,
+ form
+ use-template "StdAffil" } } } } } } } } ,
+ {
+ name "StdCitPat" ,
+ format {
+ asn1 "Cit-pat" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Cit-pat.title" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cit-pat.authors" ,
+ form
+ use-template "StdAuthList" } ,
+ {
+ asn1 "Cit-pat" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Cit-pat.country" ,
+ suffix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cit-pat.doc-type" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cit-pat.number" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cit-pat.date-issue" ,
+ prefix " (" ,
+ suffix ")" ,
+ form
+ user {
+ printfunc "StdDatePrint" } } ,
+ {
+ asn1 "Cit-pat.app-number" ,
+ prefix " Appl: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cit-pat.app-date" ,
+ prefix " (" ,
+ suffix ")" ,
+ form
+ user {
+ printfunc "StdDatePrint" } } } } } } } } } ,
+ {
+ name "StdIdPat" ,
+ format {
+ asn1 "Id-pat" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Id-pat.country" ,
+ suffix " " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Id-pat.id.number" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Id-pat.id.app-number" ,
+ prefix "Appl: " ,
+ form
+ text {
+ } } } } } } ,
+ {
+ name "StdCitLet" ,
+ format {
+ asn1 "Cit-let" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Cit-let.type" ,
+ prefix "[" ,
+ suffix "]" ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "Cit-let.man-id" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cit-let.cit" ,
+ form
+ use-template "StdCitBook" } } } } } ,
+ {
+ name "StdPubEquiv" ,
+ format {
+ asn1 "Pub-equiv" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Pub-equiv.E" ,
+ form
+ use-template "StdPub" } } } } } ,
+ {
+ name "StdTitle" ,
+ format {
+ asn1 "Title" ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Title.E.trans" ,
+ prefix "[" ,
+ suffix "]" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Title.E.name" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Title.E.tsub" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Title.E.abr" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Title.E.iso-jta" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Title.E.ml-jta" ,
+ label "MEDLINE" ,
+ prefix ": " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Title.E.jta" ,
+ label "jta" ,
+ prefix ": " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Title.E.issn" ,
+ label "ISSN" ,
+ prefix ": " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Title.E.coden" ,
+ label "CODEN" ,
+ prefix ": " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Title.E.isbn" ,
+ label "ISBN" ,
+ prefix ": " ,
+ form
+ text {
+ } } } } } } ,
+ {
+ name "StdAuthList" ,
+ format {
+ asn1 "Auth-list" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Auth-list" ,
+ form
+ user {
+ printfunc "StdAuthListNamesPrint" } } ,
+ {
+ asn1 "Auth-list.affil" ,
+ form
+ use-template "StdAffil" } } } } } ,
+ {
+ name "StdAffil" ,
+ format {
+ asn1 "Affil" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Affil.str" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Affil.std.affil" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Affil.std.div" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Affil.std.street" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Affil.std" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Affil.std.city" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Affil.std.sub" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Affil.std.country" ,
+ form
+ text {
+ } } } } } } } } } ,
+ {
+ name "StdImprint" ,
+ format {
+ asn1 "Imprint" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Imprint.date" ,
+ prefix "(" ,
+ suffix ") " ,
+ form
+ user {
+ printfunc "StdDatePrint" } } ,
+ {
+ asn1 "Imprint.volume" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Imprint.issue" ,
+ prefix " (" ,
+ suffix ")" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Imprint.section" ,
+ prefix " (" ,
+ suffix ")" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Imprint.part-sup" ,
+ prefix " (" ,
+ suffix ")" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Imprint.pages" ,
+ prefix ": " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Imprint.prepub" ,
+ prefix " (" ,
+ suffix ")" ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "Imprint.pub" ,
+ label "\nPublisher: " ,
+ form
+ use-template "StdAffil" } ,
+ {
+ asn1 "Imprint.cprt" ,
+ label " Copyright: " ,
+ form
+ user {
+ printfunc "StdDatePrint" } } } } } } ,
+ {
+ name "StdSeqFeatXref" ,
+ format {
+ asn1 "SeqFeatXref" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "SeqFeatXref.id" ,
+ label "Id=" ,
+ form
+ use-template "StdFeatId" } ,
+ {
+ asn1 "SeqFeatXref.data" ,
+ form
+ use-template "StdSeqFeatData" } } } } } ,
+ {
+ name "StdOrgRef" ,
+ format {
+ asn1 "Org-ref" ,
+ label "Org-ref" ,
+ prefix "\n" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Org-ref" ,
+ form
+ block {
+ separator " " ,
+ components {
+ {
+ asn1 "Org-ref.taxname" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Org-ref.common" ,
+ prefix "(" ,
+ suffix ")" ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "Org-ref.mod" ,
+ label "Modifiers" ,
+ prefix " (" ,
+ suffix ")" ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Org-ref.mod.E" ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "Org-ref.db" ,
+ label "Cross Reference" ,
+ prefix " " ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Org-ref.db.E" ,
+ prefix "(" ,
+ suffix ")" ,
+ form
+ use-template "StdDbtag" } } } } ,
+ {
+ asn1 "Org-ref.syn" ,
+ label "Synonyms" ,
+ prefix " (" ,
+ suffix ")" ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Org-ref.syn.E" ,
+ form
+ text {
+ } } } } } } } } } ,
+ {
+ name "StdBioSource" ,
+ format {
+ asn1 "BioSource" ,
+ label "BioSource" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "BioSource.genome" ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "BioSource.org" ,
+ label "Organism" ,
+ form
+ use-template "StdOrgRef" } } } } } ,
+ {
+ name "StdCdRegion" ,
+ format {
+ asn1 "Cdregion" ,
+ label "Cdregion" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Cdregion.orf" ,
+ form
+ boolean {
+ true "Uncharacterized Open Reading Frame" } } ,
+ {
+ asn1 "Cdregion.frame" ,
+ label "Reading Frame = " ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "Cdregion.code" ,
+ label "Genetic Code: " ,
+ suffix ";" ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Genetic-code.E.name" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Genetic-code.E.id" ,
+ label "id= " ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "Cdregion.conflict" ,
+ form
+ boolean {
+ true "Translation conflicts with protein sequence" } } ,
+ {
+ asn1 "Cdregion.stops" ,
+ prefix "Translation contains " ,
+ suffix " stop codons" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cdregion.gaps" ,
+ prefix "Translation contains " ,
+ suffix " gaps when aligned to protein" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Cdregion.mismatch" ,
+ prefix "Translation contains " ,
+ suffix " mismatches when aligned to protein" ,
+ form
+ text {
+ } } } } } } ,
+ {
+ name "StdProtRef" ,
+ format {
+ asn1 "Prot-ref" ,
+ label "Prot-ref" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Prot-ref.name" ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Prot-ref.name.E" ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "Prot-ref.desc" ,
+ prefix "[" ,
+ suffix "]" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Prot-ref.processed" ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "Prot-ref.ec" ,
+ label "ec" ,
+ prefix ": " ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Prot-ref.ec.E" ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "Prot-ref.activity" ,
+ label "activity" ,
+ prefix ": " ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Prot-ref.activity.E" ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "Prot-ref.db" ,
+ label "Cross Reference" ,
+ prefix " " ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Prot-ref.db.E" ,
+ prefix "(" ,
+ suffix ")" ,
+ form
+ use-template "StdDbtag" } } } } } } } } ,
+ {
+ name "StdRNARef" ,
+ format {
+ asn1 "RNA-ref" ,
+ label "RNA-ref" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "RNA-ref.type" ,
+ form
+ enum {
+ } } ,
+ {
+ asn1 "RNA-ref.pseudo" ,
+ form
+ boolean {
+ true "This is an RNA pseudogene." } } ,
+ {
+ asn1 "RNA-ref.ext.name" ,
+ form
+ text {
+ } } } } } } ,
+ {
+ name "StdPubdesc" ,
+ format {
+ asn1 "Pubdesc" ,
+ label "Pubdesc" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Pubdesc.pub" ,
+ form
+ use-template "StdPubEquiv" } ,
+ {
+ asn1 "Pubdesc" ,
+ prefix "In this article:\n" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Pubdesc.name" ,
+ label "name=" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Pubdesc.fig" ,
+ label "figure=" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Pubdesc.poly-a" ,
+ form
+ boolean {
+ true "poly(A) shown" } } ,
+ {
+ asn1 "Pubdesc.maploc" ,
+ label "map location=" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Pubdesc.num" ,
+ form
+ use-template "StdNumbering" } ,
+ {
+ asn1 "Pubdesc.numexc" ,
+ form
+ boolean {
+ true "numbering inconsistent" } } } } } ,
+ {
+ asn1 "Pubdesc.comment" ,
+ form
+ text {
+ } } } } } } ,
+ {
+ name "StdImpFeat" ,
+ format {
+ asn1 "Imp-feat.key" ,
+ label "Imp-feat" ,
+ form
+ text {
+ } } } ,
+ {
+ name "StdRsiteRef" ,
+ format {
+ asn1 "Rsite-ref" ,
+ label "Rsite-ref" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Rsite-ref.str" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Rsite-ref.std" ,
+ form
+ use-template "StdDbtag" } } } } } ,
+ {
+ name "StdTxInit" ,
+ format {
+ asn1 "Txinit" ,
+ label "TxInit" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Txinit.name" ,
+ form
+ text {
+ } } } } } } ,
+ {
+ name "StdNumbering" ,
+ format {
+ asn1 "Numbering" ,
+ label "Numbering" ,
+ form
+ null NULL } } ,
+ {
+ name "StdGBBlock" ,
+ format {
+ asn1 "GB-block" ,
+ label "GenBank-block" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "GB-block.extra-accessions" ,
+ label "Extra accessions" ,
+ prefix " (" ,
+ suffix ")" ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "GB-block.extra-accessions.E" ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "GB-block.keywords" ,
+ label "Keywords" ,
+ prefix " (" ,
+ suffix ")" ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "GB-block.keywords.E" ,
+ form
+ text {
+ } } } } } ,
+ {
+ asn1 "GB-block.source" ,
+ label "Source: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "GB-block.origin" ,
+ label "Origin: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "GB-block.div" ,
+ label "Division: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "GB-block.taxonomy" ,
+ label "Taxonomy: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "GB-block.date" ,
+ label "Date: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "GB-block.entry-date" ,
+ label "Entry date: " ,
+ form
+ user {
+ printfunc "StdDatePrint" } } } } } } ,
+ {
+ name "StdFeatId" ,
+ format {
+ asn1 "Feat-id" ,
+ form
+ block {
+ components {
+ {
+ asn1 "Feat-id.gibb" ,
+ label "GenInfo Backbone: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Feat-id.giim.id" ,
+ label "GenInfo Import Id: " ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Feat-id.local" ,
+ label "Local: " ,
+ form
+ use-template "StdObjectId" } ,
+ {
+ asn1 "Feat-id.general" ,
+ form
+ use-template "StdDbtag" } } } } } ,
+ {
+ name "StdSeqFeatCommon" ,
+ format {
+ asn1 "Seq-feat" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Seq-feat.id" ,
+ label "Id=" ,
+ form
+ use-template "StdFeatId" } ,
+ {
+ asn1 "Seq-feat.title" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Seq-feat" ,
+ suffix ";" ,
+ form
+ block {
+ separator ", " ,
+ components {
+ {
+ asn1 "Seq-feat.partial" ,
+ form
+ boolean {
+ true "Partial" } } ,
+ {
+ asn1 "Seq-feat.except" ,
+ form
+ boolean {
+ true "Biological Exception" } } ,
+ {
+ asn1 "Seq-feat.exp-ev" ,
+ label "Evidence" ,
+ prefix " is " ,
+ form
+ enum {
+ } } } } } ,
+ {
+ asn1 "Seq-feat.comment" ,
+ form
+ text {
+ } } ,
+ {
+ asn1 "Seq-feat.ext" ,
+ form
+ use-template "StdUserObj" } ,
+ {
+ asn1 "Seq-feat.qual" ,
+ label "Qualifiers" ,
+ prefix "\n" ,
+ form
+ block {
+ separator "\n" ,
+ components {
+ {
+ asn1 "Seq-feat.qual.E" ,
+ prefix "/" ,
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+-- services, effective 18 May 1994.
+--
+-- This key can be confirmed in several possible ways:
+-- (1) It will appear in the "data" directory on Entrez CD-ROMs release 11.0
+-- and higher
+-- (2) Beginning in June of 1994, it will appear within the NCBI toolbox
+-- on ftp.ncbinih.gov:/toolbox/ncbi_tools
+-- (3) As a last resort, if you wish to confirm this information, call
+-- (301)496-2475 and ask for "NCBI network services".
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+<HTML> <HEAD>
+
+<TITLE>Sequin help documentation</TITLE>
+
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+ <META NAME="description" CONTENT="Sequin is a stand-alone software tool developed by the National Center for Biotechnology Information (NCBI) for submitting and updating entries to the GenBank, EMBL, or DDBJ sequence databases. "> -->
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+ <td width="140"><a href="http://www.ncbi.nlm.nih.gov"> <img src="http://www.ncbi.nlm.nih.gov/corehtml/left.GIF" width="130" height="45" border="0"></a></td>
+ <td width="360" class="head1" valign="BOTTOM"> <span class="H1">Sequin Help Documentation</span></td>
+<!-- <td width="100" valign="BOTTOM">Your Logo</td> -->
+ </tr>
+</table>
+
+<!-- the quicklinks bar -->
+<table CLASS="TEXT" border="0" width="600" cellspacing="0" cellpadding="3" bgcolor="#000000">
+ <tr CLASS="TEXT" align="CENTER">
+ <td width="100"><a href="index.html" class="BAR">Sequin</a></td>
+ <td width="100"><a href="http://www.ncbi.nlm.nih.gov/Entrez/" class="BAR">Entrez</a></td>
+ <td width="100"><a href="http://www.ncbi.nlm.nih.gov/BLAST/" class="BAR">BLAST</a></td>
+ <td width="100"><a href="http://www.ncbi.nlm.nih.gov/omim/" class="BAR">OMIM</a></td>
+ <td width="100"><a href="http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html" class="BAR">Taxonomy</a></td>
+ <td width="100"><a href="http://www.ncbi.nlm.nih.gov/Structure/" class="BAR">Structure</a></td>
+ </tr>
+</table>
+
+<!-- the contents -->
+<P> 
+
+<H2>Table of Contents</H2>
+
+<HR>
+
+>Introduction
+
+#Sequin is a program designed to aid in the submission of sequences to
+the GenBank, EMBL, and DDBJ sequence databases. It was written at the
+National Center for Biotechnology Information, part of the National
+Library of Medicine at the National Institutes of Health. This section
+of the help document provides a basic overview of how to submit
+sequences using the Sequin forms. Subsequent sections provide detailed
+instructions for entering information on each form.
+
+*The Help Documentation
+
+#The Sequin help documentation is available in both on-line and World
+Wide Web (http://www.ncbi.nlm.nih.gov/Sequin/sequin.hlp.html) formats.
+The text of the on-line version scrolls as you progress through the
+Sequin forms. Specific words or phrases can be identified with the
+"find" command at the top of the window. The on-line document can also
+be saved as a text file, or printed directly to a printer. Click on the
+window that contains the help documentation. Under the Sequin File
+menu, choose Export Help... to save the documentation as a text file.
+To print the documentation without saving it first, click on the help
+window, and choose Print from the Sequin File menu.
+
+*Organization of Forms
+
+#Information is entered into Sequin on a number of different forms. Each
+form is made up of pages, which are indicated by folder tabs at the top
+of the form. You can move to the desired page by clicking on the
+appropriate folder tab. You can also move between pages of a form by
+clicking on the "Next page" or "Prev page" buttons at the bottom of the
+screen. You can move to the previous form or the next form by clicking
+on the "Prev form" or "Next form" buttons on the first or last pages of
+a form, respectively.
+
+#There are numerous ways to enter information onto a page of a form,
+#including text fields, radio buttons, check boxes, scrolling boxes,
+#pop-up menus and spreadsheets.
+
+#You may also use tables to import annotation of source information.
+#The formatting of these tables will be discussed below.
+
+*Overview of Sequin
+
+#If you are using Sequin for the first time, you will be prompted to
+fill out four forms: the Welcome to Sequin form, the Submitting
+Authors Form, the Sequence Format form, and the Organism and Sequences
+Form. After you have filled out these forms, a window will appear that
+contains the Sequin record viewer. This viewer allows you to access
+many other forms in which you can edit fields filled out in the three
+initial forms, as well as add additional information. Detailed
+instructions on how to fill out the forms and use the record viewer are
+presented below.
+
+>Welcome to Sequin Form
+
+#First, indicate with one of the three radio buttons whether you are
+submitting the sequence to the GenBank, EMBL, or DDBJ database. If you
+are working on a sequence submission for the first time, click on
+"Start New Submission". If you are modifying an existing submission
+record, click on "Read Existing Record". If you would like to quit from
+Sequin, click on "Quit Program".
+
+#You can also "Read Existing Record" to read in a FASTA-formatted
+#sequence file
+for analysis purposes. The sequence will be displayed in Sequin and
+can be analyzed with tools such as CDD Search, but it should not be
+submitted because it does not have the appropriate annotations.
+
+#If you are running Sequin in its network-aware mode, you will see
+another button labeled "Download from Entrez". This option allows you
+to update an existing database record using Sequin. The record will be
+downloaded from GenBank into Sequin using NCBI's Entrez retrieval
+system. The contents of the record will appear in Sequin, and you can
+edit them by updating the sequence or the annotations, as necessary. If
+you do not see the button labeled "Download from Entrez" on the Welcome
+to Sequin form, you are not running Sequin in its network-aware mode.
+To make Sequin network-aware, see the
+<A HREF="#NetConfigure">
+instructions
+</A>
+later in the help documentation.
+
+#You can update only those records that you have submitted, not those
+submitted by others. To update an existing record, first select which
+of the databases you will be sending the update to. This should be the
+database to which the original record was submitted. If you do not
+know which database to use, send the record to GenBank and the NCBI
+staff will forward it to the appropriate database. Next, click on the
+button "Download from Entrez". Enter the nucleotide Accession number or
+GI of the sequence on the first form. Then enter "yes" if you are
+planning to submit the record as an update to one of the databases.
+Fill out the Submitting Authors form.
+
+<A HREF="#EditSubmitterInfo">
+Instructions
+</A>
+
+for this form are found in the Sequin help documentation under "Edit
+Submitter Info" under the Sequin File menu. The record will then open
+in the record viewer. Explanations of how to add annotations or update
+sequences are presented in the documentation entitled
+
+<A HREF="#EditingtheRecord">
+"Editing the record"
+</A>
+and
+<A HREF="#SequenceEditor">
+"Sequence Editor"
+</A>
+
+ respectively. You will not see the Submitting Authors Form, the
+Sequence Format Form, or the Organism and Sequences Form. Note that
+updates, as well as new records, must be emailed to the appropriate
+database. Sequin does not support direct submission of records over the
+Internet.
+
+#Additional configuration options are available under the Misc menu.
+You can toggle between the stand-alone and network-aware modes of
+Sequin. The default mode of Sequin, which is sufficient for most
+sequence submissions, is stand-alone. In its network-aware mode, Sequin
+can exchange data with NCBI and, for example, retrieve sequences
+from Entrez and perform Taxonomy searches. The network-aware mode of
+Sequin is described in detail in the
+<A HREF="#NetConfigure">
+Net Configure
+</A>
+section below. You can also start the NCBI DeskTop, which is for
+advanced Sequin users only.
+
+>Submitting Authors Form
+
+#Information from this form will be used as a citation for the sequence
+entry itself. It can contain the same information found in citations
+associated with the formal publication of the sequence.
+
+#On the bottom of each form are two buttons. Click "Prev form" (first
+page in a form) or "Prev page" (subsequent pages in a form) to go to the
+previous form or page. Click "Next Form" (last page on a form) or "Next
+Page" (earlier pages on a form) to move to the next form or page.
+
+#Form pages can also be saved individually by using the "Export" function
+under the File menu. If you are processing multiple submissions, you
+can use the "Import" function under the File menu to paste previously
+entered information directly on the page.
+
+#The Contact, Authors, and Affiliation pages can be saved as a block so
+that you can use this information for your next submission. For your
+first Sequin submission, fill in the requested information on the
+Submitting Authors form and proceed with the preparation of the
+submission. Choose Export Submitter Info under the File menu to export
+this to a file. You can then import this information in subsequent
+submissions using the Import Submitter Info in the File menu. You will
+need to fill in the manuscript title for each submission however.
+
+*Submission Page
+
+**When May We Release Your Sequence Record?
+
+#Please select one of the two radio buttons. If you select
+#"Immediately After Processing", the
+entry will be released to the public after the database staff has added
+it to the database. If you select "Release Date", fields will appear in
+which you can indicate the date on which the sequences should be
+released to the public. The submission will then be held back until
+formal publication of the sequence or GenBank Accession number, or
+until the release date, whichever comes first.
+
+**Tentative Title for Manuscript
+
+#Please enter a title that appropriately describes the sequence entry.
+ Later in the submission process, you will have the
+opportunity to change this information and add details for published
+or in press references.
+
+*Contact Page
+
+#Please enter the name, telephone and fax numbers, and email address of
+the person who is submitting the sequence. This is the person who will
+be contacted regarding the sequence submission. The phone, fax, and
+email address will not be visible in the database record, but are
+essential for contact by the database staff.
+
+*Authors Page
+
+#Please enter the names of the people who should receive scientific
+credit for the generation of sequences in this entry. The person on
+the Contact page is automatically listed as the first author. This
+information can be changed if necessary. The author names should be
+entered in the order first name, middle initial, surname. You can add
+as many authors to this page as you wish. After you type in the name
+of the third author, the box becomes a spreadsheet, and you can scroll
+down to the next line by using the space bar. The consortium box
+should only be used for consortium names, not institute or department
+names.
+
+*Affiliation Page
+
+#Please enter information about the principal institution where the
+sequencing was performed. This is not necessarily the same as the
+workplace of the person described on the Contact page. This information
+will show up in the reference section of the record, with the title
+Direct Submission.
+
+>Sequence Format Form
+
+#Use this form to indicate the type, format and category of sequence
+#you are submitting.
+
+#Sequin can process single nucleotide sequences, gapped sequences and
+sets of related sequences. If the sequences are related in terms of
+coming from the same publication, or the same organism, they may be
+candidates for a Batch submission. Biologically related sequences may
+be classified as environmental samples, population, phylogenetic,
+mutation, or segmented sets as appropriate. Segmented sets consist of
+a collection of non-overlapping sequences covering a specific genetic
+region. In all cases, although the sequences are handled as a single
+submission, each sequence in a set will receive its own database
+Accession number and can be annotated independently.
+
+#Sequin can display the alignments of sequences that are submitted as
+part of an aligned phylogenetic, population, mutation set, or
+environmental samples. Such sequences can be submitted in FASTA,
+Contiguous (FASTA+GAP, NEXUS, MACAW), or Interleaved (PHYLIP, NEXUS)
+formats. If the sequences are in FASTA format, Sequin can generate an
+alignment. If the sequences have already been aligned in FASTA+GAP,
+PHYLIP, MACAW, or NEXUS, Sequin will not change the alignment. If one
+of the sequences in your alignment is already present in the
+GenBank/EMBL/DDBJ database, you must mark that sequence so that it does
+not receive a new Accession number. Instead of supplying that sequence
+with a new Sequence Identifier, give it the identifier accU12345, where
+U12345 is the Accession number of the sequence.
+
+#Single sequences, gapped sequences, segmented sequences, and batch
+submissions must be submitted in FASTA format.
+
+*Submission Type
+
+#Use the radio buttons to indicate which of the following types of
+submissions you are creating:
+
+#-Single sequence: a single mRNA or genomic DNA sequence. If you are
+submitting multiple sequences from the same publication, consider a
+Batch Submission. If you decide to submit multiple Sequin files, each
+with one or more sequences, please send each file in a separate email
+message.
+
+#-Segmented sequence: a collection of non-overlapping, non-contiguous
+sequences that cover a specified genetic region. A standard example is
+a set of genomic DNA sequences that encode exons from a gene along with
+fragments of their flanking introns. If the segmented set is part of
+an alignment, however, select the appropriate Population, Phylogenetic,
+or Mutation study button.
+
+#-Gapped sequence: a single, non-contiguous mRNA or genomic DNA sequence.
+A gapped sequence contains specified gaps of know or unknown length
+where the exact nucleotide sequence has not been determined. The FASTA
+format for gapped sequences is slightly different and is explained
+below.
+
+#-Population study: a set of sequences that were derived by sequencing
+the same gene from different isolates of the same organism.
+
+#-Phylogenetic study: a set of sequences that were derived by sequencing
+the same gene from different organisms.
+
+#-Mutation study: a set of sequences that were derived by sequencing
+multiple mutations of a single gene.
+
+#-Environmental samples: a set of sequences that were derived by
+sequencing the same gene from a population of unclassified or unknown
+organisms.
+
+#-Batch submission: a set of related sequences that are not part of a
+population, mutation, or phylogenetic study. The sequences should be
+related in some way, such as coming from the same publication or
+organism. You should plan that all sequences will be released to the
+public on the same date.
+
+*Sequence Data Format
+
+#If you are submitting a single, gapped, or segmented sequence, or a
+batch submission, your sequence must be in FASTA format, described
+below. If you are submitting a set of sequences as part of a
+population, phylogenetic, or mutation study, you have a choice of
+sequence formats. You may submit the set as individual sequences in
+FASTA format. Alternatively, you can submit the sequences as part of
+an alignment. Sequin currently accepts the alignment formats
+FASTA+GAP, PHYLIP, MACAW, NEXUS Interleaved, and NEXUS Contiguous.
+
+*Submission Category
+
+#Use the radio buttons to indicate whether your sequence corresponds to
+an original submission or a third-party annotation submission. If you
+have directly sequenced the nucleotide sequence in your laboratory,
+your submission would be considered an original submission.
+
+#If you have downloaded the sequence from GenBank and added to it your
+own annotations, your entry may be eligible for submission to the
+Third-Party Annotation Database
+
+<A HREF="http://www.ncbi.nlm.nih.gov/Genbank/tpa.html">
+(TPA)
+</A>
+.
+
+#In order to be released into the TPA database, the sequence must appear
+in a peer-reviewed publication in a biological journal. If you select
+this option, a pop-up box will appear upon the completion of the
+Sequence Format form. You must provide some description of the
+biological experiments used as evidence for the annotation of your TPA
+submission in this box.
+
+#You will be asked later in the submission process to provide the GenBank
+Accession number(s) of the primary sequence(s) from which your TPA
+submission was derived.
+
+>Organism and Sequences Form
+
+#This form is made up of four pages. If your sequences are imported as
+properly formatted FASTA files, there will be minimum input necessary
+in these pages.
+
+>FASTA Format for Nucleotide Sequences
+
+#In FASTA format the line before the nucleotide sequence, called the
+FASTA definition line, must begin with a carat (">"), followed by a
+unique SeqID (sequence identifier). The SeqID must be unique for each
+nucleotide sequence and should not contain any spaces. Use of brackets
+("[]") in the SeqID is also prohibited. The identifier will be
+replaced with an Accession number by the database staff when your
+submission is processed.
+
+#Information about the source organism from which the sequence was
+obtained follows the SeqID and must be in the format [modifier=text].
+Do not put spaces around the "=". At minimum, the scientific name of
+the organism should be included. Optional modifiers can be added to
+provide additional information. A complete list of available source
+<A HREF="http://www.ncbi.nlm.nih.gov/Sequin/modifiers.html">
+modifiers
+</A>
+ and their format is available.
+
+#The final optional component of the FASTA definition line is the
+sequence title, which will be used as the DEFINITION field in the final
+flatfile. The title should contain a brief description of the
+sequence. There is a preferred format for nucleotide and protein
+titles and Sequin can generate them automatically using the Generate
+Definition Line function under the Annotate menu in the record viewer.
+
+#Note in all cases, the FASTA definition line must not contain any hard
+returns. All information must be on a single line of text. If you
+have trouble importing your FASTA sequences, please double check that
+no returns were added to the FASTA definition line by your editing
+software.
+
+#Examples of properly formatted FASTA definition lines for nucleotide
+sequences are:
+
+<KBD><PRE>>Seq1 [organism=Mus musculus] [strain=C57BL/6] Mus musculus neuropilin 1 (Nrp1) mRNA, complete cds.
+</KBD></PRE>
+<KBD><PRE>>ABCD [organism=Plasmodium falciparum] [isolate=ABCD] Plasmodium falciparum isolate ABCD merozoite surface protein 2 (msp2) gene, partial cds.
+</KBD></PRE>
+<KBD><PRE>>DNA.new [organism=Homo sapiens] [chromosome=17] [map=17q21] [moltype=mRNA] Homo sapiens breast and ovarian cancer susceptibility protein (BRCA1) mRNA, complete cds.
+</KBD></PRE>
+#The line after the FASTA definition line begins the nucleotide
+sequence. Unlike the FASTA definition line, the nucleotide sequence
+itself can contain returns. It is recommended that each line of
+sequence be no longer than 80 characters. Please only use IUPAC
+symbols within the nucleotide sequence. For sequences that are not
+contained within an alignment, do not use "?" or "-" characters. These
+will be stripped from the sequence. Use the IUPAC approved symbol "N"
+for ambiguous characters instead.
+
+#A single file containing multiple FASTA sequences can be imported into
+Sequin. Make sure that the FASTA definition line for each sequence is
+formatted as above.
+
+#If the FASTA definition line is not properly formatted a pop-up box
+will appear upon importing the nucleotide FASTA. The top box in this
+pop-up will list any errors in the FASTA definition lines, including
+missing SeqIDs, duplicate SeqIDs for different sequences, or improperly
+formatted modifiers. You can add or edit this information in the
+spreadsheet provided. The toggle at the bottom of the pop-up allows
+you to select whether all sequences or only those with errors are
+listed in the spreadsheet above. After making changes, click on Refresh
+Error List to ensure that all errors have been corrected. You must
+correct any errors involving the SeqID in order to proceed with your
+submission.
+
+*FASTA Format for Segmented Sequence
+
+#Each segment of a segmented sequence must have its own SeqID, but the
+organism name and other modifiers are only indicated in the FASTA
+definition line of the first segment. Square brackets are used to
+delimit the members of the segmented set. For example,
+
+![
+!>A-0V-1-Apart1 [organism=Gallus gallus] [clone=C]
+!TCACTCTTTGGCAAC
+!>A-0V-1-Apart2
+!GACCCGTCGTCATAATAAAGATAGAGGGGCAACTAAAGGAAGCTCTA
+!TTAGATACAGGAGCAGATGATACAGTATTAGAAGAAAT
+!]
+
+*FASTA Format for Gapped Sequence
+
+#The FASTA definition line for a gapped sequence follows the same format
+as above. To indicate a gap within the sequence, enter a hard return
+within the sequence at the point of the gap, then insert an extra line
+starting with a carat (">") and a question mark ("?"). If the gap size
+is unknown, enter "unk100" after the question mark. If the gap size is
+known, enter the length of the gap after the question mark. For
+example,
+
+!>Dobi [organism=Canis familiaris] [breed=Doberman pinscher]
+!AAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTTAGCCCAGAAGTAATACCCATGTTTTCAGCATTA
+!GGAAAAAGGGCTGTTG
+!>?unk100
+!TGGATGACAGAAACCTTGTTGGTCCAAAATGCAAACCCAGATKGTAAGACCATTTTAAAAGCATTGGGTC
+!TTAGAAATAGGGCAACACAGAACAAAAAT
+!>?234
+!AAAAATAAAAGCATTAGTAGAAATTTGTACAGAACTGGAAAAGGAAGGAAAAATTTCAAAAATTGGGCCT
+!GAAAACCCATACAATACTCCGGG
+
+will generate a sequence containing two gaps. The first gap is of
+unknown length, the second is 234 nucleotides long.
+
+*FASTA+GAP Format for Aligned Nucleotide Sequences
+
+#A number of programs output sets of aligned sequences in FASTA format.
+Frequently, to align these sequences, gaps must be inserted. Specify
+relevant gap and ambiguous characters in the appropriate box on the
+
+<A HREF="#NucleotidePage">
+Nucleotide Page
+</A>
+
+form. Each sequence, including gaps, must be the same length. The
+gaps will only show up in the alignment, not in the individual sequence
+in the database.
+
+#Sequences in FASTA+GAP format resemble FASTA sequences. The previous
+section on
+
+<A HREF="#FASTAFormatforNucleotideSequences">
+FASTA Format for Nucleotide Sequences
+</A>
+
+has instructions for formatting FASTA sequences. If one of the
+sequences in your alignment is already present in the GenBank/EMBL/DDBJ
+database, you must mark that sequence so that it does not receive a new
+Accession number. To do this, use a SeqID in the format accU12345,
+where U12345 is the Accession number of the pre-existing sequence. All
+sequences in FASTA+GAP format should be in the same file.
+
+#The following is an example of FASTA+GAP format:
+
+!>A-0V-1-A [organism=Gallus gallus] [clone=C]
+!TCACTCTTTGGCAACGACCCGTCGTCATAATAAAGATAGAGGGGCAACTAAAGGAAGCTCTA
+!TTAGATACAGGAGCAGATGATACAGTATTAGAAGAAAT
+!
+!>A-0V-2-A [organism=Drosophila melanogaster] [strain=D]
+!TCACTCTTTGGCAAC---GCGTCGTCACAATAAAGATAGAGGGGCAACTAAAGGAAGCTCTA
+!TTAGATACAGGAGCAGATGATACAGTATTAGAAGAAAT
+!
+!>A-0V-3-A [organism=Caenorhabditis elegans] [strain=E]
+!TCACTCTTTGGCAAC---GCGTCGTCACAATAAAGATAGAGGGGCAACTAAAGGAAGCTCTA
+!TTAGATACAGGAGCAGATGATACAGTATTAGAAGAAAT
+!
+!>A-0V-4-A [organism=Rattus norvegicus] [strain=F]
+!TCACTCTTTGGCAACGACCCGTCGTCACAATAAAGATAGAGGGGCAACTAAAGGAAGCTCTA
+!TTAGATACAGGAGCAGATGATACAGTATTAGAAGAAAT
+!
+!>A-0V-7-A [organism=Aspergillus nidulans] [strain=G]
+!TCACTCTTTGGCAACGACCAGTCGTCACAATAAAGATAGAGGGGCAACTAAAGGAAGCTCTA
+!TTAGATACAGGAGCAGATGATACAGTATTAGAAGAAAT
+
+*PHYLIP Format for Aligned Nucleotide Sequences
+
+#A number of programs output sets of aligned sequences in PHYLIP format.
+
+#The following is an example of PHYLIP format.
+
+! 5 100
+!A-0V-1-A TCACTCTTTG GCAACGACCC GTCGTCATAA TAAAGATAGA GGGGCAACTA
+!A-0V-2-A TCACTCTTTG GCAAC---GC GTCGTCACAA TAAAGATAGA GGGGCAACTA
+!A-0V-3-A TCACTCTTTG GCAAC---GC GTCGTCACAA TAAAGATAGA GGGGCAACTA
+!A-0V-4-A TCACTCTTTG GCAACGACCC GTCGTCACAA TAAAGATAGA GGGGCAACTA
+!A-0V-7-A TCACTCTTTG GCAACGACCA GTCGTCACAA TAAAGATAGA GGGGCAACTA
+!
+!
+! AAGGAAGCTC TATTAGATAC AGGAGCAGAT GATACAGTAT TAGAAGAAAT
+! AAGGAAGCTC TATTAGATAC AGGAGCAGAT GATACAGTAT TAGAAGAAAT
+! AAGGAAGCTC TATTAGATAC AGGAGCAGAT GATACAGTAT TAGAAGAAAT
+! AAGGAAGCTC TATTAGATAC AGGAGCAGAT GATACAGTAT TAGAAGAAAT
+! AAGGAAGCTC TATTAGATAC AGGAGCAGAT GATACAGTAT TAGAAGAAAT
+
+#In this example, the first line indicates that there are 5 sequences,
+each with 100 nt of sequence. The following five lines contain the
+Sequence IDs, followed by the sequences. Specifically, the sequence
+identifier for the first sequence is A-0V-1-A. Note that subsequent
+blocks of sequence do not contain the Sequence ID. If one of the
+sequences in your alignment is already present in the GenBank/EMBL/DDBJ
+database, you must mark that sequence so that it does not receive a new
+Accession number. To do this, use a SeqID in the format accU12345,
+where U12345 is the Accession number of the pre-existing sequence.
+
+#Specify relevant gap and ambiguous characters in the appropriate box on the
+<A HREF="#NucleotidePage">
+Nucleotide Page
+</A>
+form.
+
+#You can modify the PHYLIP format so that Sequin can
+determine the correct organism and any other modifiers for each
+sequence. An example of such modifications are below in the section on
+<A HREF="#SourceModifiersforPHYLIPandNEXUS">
+Source Modifiers for PHYLIP and NEXUS
+</A>
+.
+#Alternatively, you can leave your sequence alignment in
+standard PHYLIP format and enter the organism, strain, chromosome, etc.
+information on the following
+
+<A HREF="#SourceModifiersForm">
+Source Modifers form
+</A>
+.
+
+*NEXUS Format for Aligned Nucleotide Sequences
+
+#A number of programs output sets of aligned sequences in one of two
+NEXUS formats, NEXUS Interleaved and NEXUS Contiguous.
+
+#NEXUS files can contain ? for "missing" at the 5' and 3' ends of
+sequences, as long as this parameter is properly defined within the
+header of the NEXUS file.
+
+#The following is an example of NEXUS Interleaved format.
+
+!#NEXUS
+!
+!begin data;
+! dimensions ntax=5 nchar=100;
+! format datatype=dna missing=? gap=- interleave;
+! matrix
+!
+!A-0V-1-A TCACTCTTTG GCAACGACCC GTCGTCATAA TAAAGATAGA GGGGCAACTA
+!A-0V-2-A TCACTCTTTG GCAAC---GC GTCGTCACAA TAAAGATAGA GGGGCAACTA
+!A-0V-3-A TCACTCTTTG GCAAC---GC GTCGTCACAA TAAAGATAGA GGGGCAACTA
+!A-0V-4-A TCACTCTTTG GCAACGACCC GTCGTCACAA T????ATAGA GGGGCAACTA
+!A-0V-7-A TCACTCTTTG GCAACGACCA GTCGTCACAA TAAAGATAGA GGGGCAACTA
+!
+!
+!A-0V-1-A AAGGAAGCTC TATTAGATAC AGGAGCAGAT GATACAGTAT TAGAAGAAAT
+!A-0V-2-A AAGGAAGCTC TATTAGATAC AGGAGCAGAT GATACAGTAT TAGAAGAAAT
+!A-0V-3-A AAGGAAGCTC TATTAGATAC AGGAGCAGAT GATACAGTAT TAGAAGAAAT
+!A-0V-4-A AAGGAAGCTC TATTAGATAC AGGAGCAGAT GATACAGTAT TAGAAGAAAT
+!A-0V-7-A AAGGAAGCTC TATTAGATAC AGGAGCAGAT GATACAGTAT TAGAAGAAAT
+
+#In this example, the first few lines provide information about the data
+in the sequence alignment. The following five lines contain the
+Sequence IDs, followed by the sequences. Specifically, the sequence
+identifier for the first sequence is A-0V-1-A. Note that subsequent
+blocks of sequence also contain the Sequence ID. If one of the
+sequences in your alignment is already present in the GenBank/EMBL/DDBJ
+database, you must mark that sequence so that it does not receive a new
+Accession number. To do this, use a SeqID in the format accU12345,
+where U12345 is the Accession number of the pre-existing sequence.
+Also, Sequin will replace the "?" characters in the sequences with "N"s
+since they are defined as "missing" data in the header. You should
+specify relevant gap and ambiguous characters in the appropriate box on
+the
+
+<A HREF="#NucleotidePage">
+
+Nucleotide Page
+
+</A>
+
+form.
+#The following is an example of NEXUS Contiguous format.
+
+!#NEXUS
+!BEGIN DATA;
+!DIMENSIONS NTAX=5 NCHAR=100;
+!FORMAT MISSING=? GAP=- DATATYPE=DNA ;
+!MATRIX
+!
+!A-0V-1-A
+!TCACTCTTTGGCAACGACCCGTCGTCATAATAAAGATAGAGGGGCAACTAAAGGAAGCTCTA
+!TTAGATACAGGAGCAGATGATACAGTATTAGAAGAAAT
+!
+!A-0V-2-A
+!TCACTCTTTGGCAAC---GCGTCGTCACAATAAAGATAGAGGGGCAACTAAAGGAAGCTCTA
+!TTAGATACAGGAGCAGATGATACAGTATTAGAAGAAAT
+!
+!A-0V-3-A
+!TCACTCTTTGGCAAC---GCGTCGTCACAATAAAGATAGAGGGGCAACTAAAGGAAGCTCTA
+!TTAGATACAGGAGCAGATGATACAGTATTAGAAGAAAT
+!
+!A-0V-4-A
+!TCACTCTTTGGCAACGACCCGTCGTCACAATAAAGATAGAGGGGCAACTAAAGGAAGCTCTA
+!TTAGATACAGGAGCAGATGATACAGTATTAGAAGAAAT
+!
+!A-0V-7-A
+!TCACTCTTTGGCAACGACCAGTCGTCACAATAAAGATAGAGGGGCAACTAAAGGAAGCTCTA
+!TTAGATACAGGAGCAGATGATACAGTATTAGAAGAAAT
+
+#In this example, the first few lines provide information about the data
+in the sequence alignment. The following five lines contain the
+Sequence IDs, followed by the sequences. Specifically, the sequence
+identifier for the first sequence is A-0V-1-A. Note that subsequent
+blocks of sequence also contain the Sequence ID. If one of the
+sequences in your alignment is already present in the GenBank/EMBL/D
+DBJ database, you must mark that sequence so that it does not receive a
+new Accession number. To do this, use a SeqID in the format accU12345,
+where U12345 is the Accession number of the pre-existing sequence.
+
+#You can modify either NEXUS format so that Sequin can
+determine the correct organism and any other modifiers for each
+sequence. An example of such modifications are below in the section on
+<A HREF="#SourceModifiersforPHYLIPandNEXUS">
+Source Modifiers for PHYLIP and NEXUS
+</A>
+.
+Alternatively, you can leave your sequence alignment in
+standard NEXUS format and enter the organism, strain, chromosome, etc.
+information on the following
+
+<A HREF="#SourceModifiersForm">
+Source Modifers form
+</A>
+.
+
+**Source Modifiers for PHYLIP and NEXUS
+
+#You can modify the PHYLIP or NEXUS formats so that Sequin can determine
+the correct organism and any other modifiers for each sequence by
+adding lines at the end of the file. The first line applies to the
+first sequence, the second line to the second sequence, and so on. You
+must have one line for each sequence. These inserted lines contain
+modifiers formatted like in the FASTA definition line, but do not begin
+with a SeqID. Instead, the SeqID is present at the beginning of the
+sequence lines as shown above.
+
+#Each of the initial lines starts with the character ">". The
+scientific organism name follows in brackets. Optional modifiers also
+follow in brackets. For further information on the data that can go in
+the lines preceding the sequences, see the instructions entitled "FASTA
+Format for Nucleotide Sequences",
+
+<A HREF="#FASTAFormatforNucleotideSequences">
+above.
+</A>
+
+#The following lines indicating the organisms and strain of each sequence
+would follow immediately after the sequence in the PHYLIP and NEXUS
+examples, above.
+
+!>[organism=Gallus gallus] [clone=C]
+!>[organism=Drosophila melanogaster] [strain=D]
+!>[organism=Caenorhabditis elegans] [strain=E]
+!>[organism=Rattus norvegicus] [strain=F]
+!>[organism=Aspergillus nidulans] [strain=G]
+
+#The number of lines of source information must exactly match the number
+of sequences provided.
+
+#Alternatively, you can leave your sequence alignment in
+standard NEXUS or PHYLIP format and enter the organism, strain, chromosome, etc.
+information on the following
+
+<A HREF="#OrganismPage">
+Organism Page
+</A>
+.
+
+*Importing Aligned Sets of Segmented Sequences
+
+#Sequin can also read segmented sets that are part of an alignment if
+the sequences are in FASTA or FASTA+GAP format. Each segment should
+have its own Sequence ID, but organism name and source modifiers should
+only be indicated for the first segment from each sequence. Square
+brackets are used to delimit the members of a set. For example,
+
+![
+!>A-0V-1-Apart1 [organism=Gallus gallus] [strain=C]
+!TCACTCTTTGGCAAC
+!>A-0V-1-Apart2
+!GACCCGTCGTCATAATAAAGATAGAGGGGCAACTAAAGGAAGCTCTA
+!TTAGATACAGGAGCAGATGATACAGTATTAGAAGAAAT
+!]
+![
+!>A-0V-2-Apart1 [organism=Drosophila melanogaster] [strain=D]
+!TCACTCTTTGGCAAC
+!>A-0V-2-Apart2
+!GAAGCGTCGTCACAATAAAGATAGAGGGGCAACTAAAGGAAGCTCTA
+!TTAGATACAGGAGCAGATGATACAGTATTAGAAGAAAT
+!]
+
+>Nucleotide Page
+
+#The options on this page will vary depending on the
+<A HREF="#SubmissionType">
+Submission Type
+</A>
+ and
+<A HREF="#SequenceDataFormat">
+Sequence Data Format
+</A>
+selected earlier. Segmented sets and gapped sequences mut be imported
+as properly formatted FASTA files. Details about importing alignment
+files are
+<A HREF="#NucleotidePageforAlignedDataFormats">
+below
+</A>
+.
+
+*Nucleotide Page for FASTA Data Format
+
+**Create Alignment
+
+#If you have selected a Population study, Phylogenetic study, Mutation
+study, or Environmental samples set as a
+<A HREF="#SubmissionType">
+Submission Type
+</A>
+a check box will appear at the top of the Nucleotide Page. If you
+check 'Create Alignment', Sequin will attempt to generate an alignment
+of the seqeunces within your submission.
+
+**Import Nucleotide FASTA
+
+#Use this button to import your properly formatted
+<A HREF="#FASTAFormatforNucleotideSequences">
+FASTA file
+</A>
+. You will see a window containing information about the imported
+sequence(s). Please check the number of sequences, Sequence IDs
+(SeqIDs) and length of each sequence to make sure they are correct. If
+you have included source information within the FASTA definition line,
+this will also be listed.
+
+**Add/Modify Sequences
+
+#This option allows you to add or modify sequences without using a
+previously formatted FASTA file, but is not available if you have
+selected a Segmented sequence or Gapped sequence as a
+<A HREF="#SubmissionType">
+Submission Type
+</A>
+. On the Specify Sequences box you can either import a nucleotide FASTA
+or add a new sequence. If you choose Add New Sequence, a new box will
+pop-up where you can either import an existing sequence file or
+directly paste or type the nucleotide sequence.
+
+#If you add a sequence where the FASTA definition line is not properly
+formatted a pop-up box will appear. The top box in this pop-up will
+list any errors in the FASTA definition lines, including missing
+SeqIDs, duplicate SeqIDs for different sequences, or improperly
+formatted modifiers. You can add or edit this information in the
+spreadsheet provided. The toggle at the bottom of the pop-up allows
+you to select whether all sequences or only those with errors are
+listed in the spreadsheet above. After making changes, click on
+Refresh Error List to ensure that all errors have been corrected. You
+must correct any errors involving the SeqID in order to proceed with
+your submission. Click on Accept to save your sequences and return to
+the Specify Sequences box.
+
+#In the Specify Sequences box, you can choose to add another sequence or
+select a sequence from the list and choose to edit or delete it. You
+can also delete all sequences at this point. You will need to click on
+Done to save your sequences and return to the Nucleotide Page.
+
+**Clear Sequences
+
+#This option will remove all imported nucleotide sequences.
+
+**Specify Molecule
+
+#A database sequence can represent one of several different molecule
+types. The default molecule is genomic DNA. If the sequence was not
+derived from genomic DNA, you can edit that information here. If you
+are submitting multiple sequences you can apply one molecule type to
+all sequences or apply the molecule type to each sequence individually.
+ Enter in the Molecule pop-up menu the type of molecule that was
+sequenced.
+
+#-Genomic DNA: Sequence derived directly from the DNA of an organism.
+Note: The DNA sequence of an rRNA gene has this molecule type, as does
+that from a naturally-occurring plasmid.
+
+#-Genomic RNA: Sequence derived directly from the genomic RNA of certain
+organisms, such as viruses.
+
+#-Precursor RNA: An RNA transcript before it is processed into mRNA,
+rRNA, tRNA, or other cellular RNA species.
+
+#-mRNA[cDNA]: A cDNA sequence derived from mRNA.
+
+#-Ribosomal RNA: A sequence derived from the RNA in ribosomes. This
+should only be selected if the RNA itself was isolated and sequenced.
+If the gene for the ribosomal RNA was sequence, select Genomic DNA.
+
+#-Transfer RNA: A sequence derived from the RNA in a transfer RNA, for
+example, the sequence of a cDNA derived from tRNA.
+
+#-Small nuclear RNA: A sequence derived from small nuclear RNA, for
+example, the sequence of a cDNA derived from snRNA.
+
+#-Small cytoplasmic RNA: A sequence derived from small cytoplasmic RNA,
+for example, the sequence of a cDNA derived from small cytoplasmic RNA.
+
+#-Other-Genetic: A synthetically derived sequence including cloning
+vectors and tagged fusion constructs.
+
+#-cRNA: A sequence derived from complementary RNA transcribed from DNA,
+mainly used for viral submissions.
+
+#-Small nucleolar RNA: A sequence derived from small nucleolar RNA, for
+example, the sequence of a cDNA derived from snoRNA.
+
+**Specify Topology
+
+#Most sequences have a Linear topology and this is the default. You
+should change this setting to Circular only if the sequence is complete
+and it has a circular topology. For example, a complete plasmid or a
+complete mitochondrial genome would have a Circular topology, but a
+single gene from a plasmid or mitochondrion would have a Linear
+topology. If you are submitting multiple sequences you can apply one
+topology to all sequences or set the topology for each sequence
+individually.
+
+*Nucleotide Page for Aligned Data Formats
+
+**Sequence Characters
+
+#If you are submitting a set of aligned sequences, you can specify sequence
+characters used in your alignment here. Sequin requires that you
+define any non-IUPAC nucleotide characters in your alignment file. The
+five types of variable characters are listed under Sequence Characters.
+
+#Every sequence within an alignment file must contain the same number of
+characters (nucleotides + gaps). Gap characters are used to represent the
+spaces between contiguous nucleotides in an alignment. Gaps that appear at
+the beginning or end of a sequence are treated differently than gaps that
+appear between nucleotides and each must be defined. GenBank prefers to
+use a hyphen (-) to represent gaps. If you use a different character to
+represent a gap, you will need to add this character to the list in the
+Beginning Gap, Middle Gap, or End Gap boxes.
+
+#Ambiguous characters represent nucleotides that are known to exist, but
+whose identity has not been experimentally validated. GenBank prefers to
+use 'n' to represent any ambiguous nucleotides. If you are using a
+different character to represent an ambiguous base, you will need to add
+this character to the list in the Ambiguous/Unknown box. Sequin will
+convert these characters to 'n's when your file is imported.
+
+#Match characters denote nucleotides that are identical in every member of
+an alignment. GenBank prefers the use of a colon (:) to represent match
+characters. If you are using a different character to represent a match
+character, you will need to add this character to the list in the Match box.
+
+**Import Nucleotide Alignment
+
+#Once you have imported the alignment using the Import Nucleotide
+Alignment button, you can edit the molecule information using the
+<A HREF="#SpecifyMolecule">
+Specify Molecule
+</A>
+ and
+<A HREF="#SpecifyTopology">
+Specify Topology
+</A>
+buttons explained above. Note that you can not access the
+<A HREF="#Add/ModifySequences">
+Add/Modify Sequences
+</A>
+ dialog for submissions of aligned sequences.
+
+>Organism Page
+
+#Information about the organism from which the sequence was derived
+should be entered or edited on this page. If there are any potential
+problems with the organism information previously provided in either
+the
+<A HREF="#FASTAFormatforNucleotideSequences">
+FASTA definition line
+</A>
+ or entered in the
+<A HREF="#Add/ModifySequences">
+Add/Modify Sequences
+</A>
+ dialog, a window listing these problems will appear at the top of the
+form. Please review these problems and edit using the
+
+<A HREF="#AddSourceModifiers">
+</A>
+Add Source Modifiers button as necessary. At minimum, you must supply
+the scientific name of the organism from which the sequence was
+obtained in order to proceed with your submission.
+
+#The second window is a summary of the organism information provided so
+far. Double clicking on a line of text within this window will launch a
+modifier-specific editing window. In each of these windows, you can
+edit the available information for the specific modifier. In most
+cases, you have the choice to edit the modifier for each sequence
+separately, or to enter text and select Apply above value to all
+sequences. These changes will be reflected in the windows of the
+Organism page immediately upon closing the modifier-specific editor.
+
+*Add Organisms, Locations, and Genetic Codes
+
+#If you have not added organism information using either the
+<A HREF="#FASTAFormatforNucleotideSequences">
+FASTA definition line
+</A>
+ or the
+<A HREF="#Add/ModifySequences">
+Add/Modify Sequences
+</A>
+dialog, you can use the Add Organisms, Locations, and Genetic Codes to
+do so at this point. This button will launch the Multiple Organism
+Editor pop-up where you may add or edit existing information concerning
+the
+<A HREF="#Organism">
+Organism
+</A>
+ name,
+<A HREF="#Location">
+Location
+</A>
+ and
+<A HREF="#GeneticCode">
+Genetic Code
+</A>
+. The SeqID of each sequence is listed at the left of the spreadsheet
+format. You can change the information in the spreadsheet individually
+or globally for all sequences.
+
+**Organism
+
+#The scrollable list at the top of the pop-up contains the scientific
+names of many organisms. To reach a name on the list, type the first
+few letters of the scientific name into the box above the list or the
+appropriate box in the spreadsheet. The list will scroll to the names
+beginning with those letters, and you can select the organism within
+the list itself. You can then use the arrow button to copy this name
+into the appropriate box in the spreadsheet.
+
+#To apply the same scientific name to all sequences in the submission,
+click on the Organism button in the spreadsheet column header. A
+separate pop-up box will appear with the same organism list. You can
+select a name from this list and choose Accept to apply this name to
+all sequences.
+
+#If you have any questions about the scientific name of an organism, see
+the NCBI
+<A HREF="http://www.ncbi.nlm.nih.gov/Taxonomy/tax.html">
+Taxonomy Browser
+</A>
+http://www.ncbi.nlm.nih.gov/Taxonomy/tax.html
+
+#If the name of the organism is not on the list, type it in directly. If
+you do not know the scientific name, please be as specific as you can
+and include a unique identifier, such as a clone, isolate, strain or
+voucher number, or cultivar name, e.g.; Nostoc ATCC29106, uncultured
+spirochete Im403, Lauraceae sp. Vásquez 25230 (MO), Rosa hybrid
+cultivar 'Kazanlik'. Also, if applicable, indicate if the name is
+unpublished as of the time of submission. Additional information such
+as strain, isolate, or serotype can be entered later in the submission
+process.
+
+**Location
+
+#The default Location for all seqeunces is "Genomic". If the sequence
+is not genomic, select the alternative location (ie, organelle) from
+the pull-down list. You can change the location of all sequences
+globally by clicking on the Location button in the spreadsheet header.
+The following is a brief description of the choices in this list:
+
+#-Genomic: chromosome. This category includes
+mitochondrial and chloroplast proteins that are encoded by the nuclear
+genome.
+
+#-Chloroplast: a chlorophyllous plastid.
+
+#-Chromoplast: a non-chlorophyllous, pigmented plastid, found in
+fruits and flowers.
+
+#-Kinetoplast: a specialized type of mitochondrion found exclusively
+in Kinetoplastida (e.g., Leishmania). NOTE: kinetoplast should
+be applied ONLY to members of the Kinetoplastida (trypanosomes and
+bodonids).
+
+#-Mitochondrion: a semi-autonomous, self-reproducing organelle that
+occurs in the cytoplasm of most eukaryotic cells.
+
+#-Plastid: any of a class of double membrane-bound, light-harvesting
+organelles (or derived from same). NOTE: plastid should be used
+ONLY when a more precise term, e.g., chloroplast, is not
+applicable.
+
+#-Macronuclear: a specialized type of nucleus found exclusively in the
+ciliated protists (e.g., Tetrahymena). NOTE: macronucleus
+should be applied ONLY to members of the Ciliophora.
+
+#-Extrachromosomal: other extrachromosomal elements not listed here,
+such as a B chromosome or an F factor.
+
+#-Plasmid: extrachromosomal genetic element found in bacterial species.
+Note this does not include the cloning vector used to propagate
+the sequence of interest.
+
+#-Cyanelle: a specialized type of plastid found exclusively in
+glaucocystophytes (e.g., Cyanophora). NOTE: cyanelle should be
+applied ONLY to members of the Glaucocystophyceae.
+
+#-Proviral: a virus that is integrated into a host cell chromosome.
+
+#-Virion: a completed virus particle.
+
+#-Nucleomorph: a reduced nuclear remnant found in Chlorarachniophyceae
+(e.g., Chlorarachnion) and Cryptophyta (e.g, Cryptomonas). NOTE:
+nucleomorph should be applied ONLY to members of the
+Chlorarachniophyceae or Cryptophyta.
+
+#-Apicoplast: a reduced plastid characteristic of apicomplexans
+(e.g., Plasmodium). NOTE: apicoplast should be applied ONLY to
+members of the Apicomplexa.
+
+#-Leucoplast: a plastid lacking pigments of any type.
+
+#-Proplastid: an immature plastid.
+
+#-Endogenous_virus: a virus that has integrated permanently into the
+host genome, and which is inherited vertically through the
+germ-line of the host.
+
+#-Hydrogenosome: an organelle that produces hydrogen and ATP and is
+found mainly in ciliates, fungi and trichomonads. Hydrogenosomes may
+be reduced mitochondria
+
+**Genetic Code
+
+#If you selected a scientific organism name from the scrollable list
+described above, this field will be filled out automatically. However,
+if the organism is not on the list, this field will default to the
+"Standard" genetic code. If this is incorrect, you can select the
+correct genetic code from the pull-down list. To globally change the
+genetic code for all sequences which are not automatically filled out,
+click on the Genetic Code button in the spreadsheet header.
+
+#For more information regarding the genetic codes available, see the NCBI
+<A HREF="http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c">
+Taxonomy page
+</A>.
+http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c
+
+*Import Source Modifiers
+
+#Using this button allows you to import a tab-delimited table of source
+modifiers. The first column in the table must contain the Sequince
+Identifiers (SeqIDs) used earlier in the submission and each subsequent
+column must contain a different source modifier. The first row in the
+table must contain the labels for each column. The label for the
+Sequence Identifiers column should be in the format "Seq_ID". A list
+of available
+<A HREF="http://www.ncbi.nlm.nih.gov/Sequin/modifiers.html">
+modifiers
+</A>
+in the format to be used in the column headers can be found at
+http://www.ncbi.nlm.nih.gov/Sequin/modifiers.html .
+
+*Add Source Modifiers
+
+#Using this button will launch the Specify Source Modifiers pop-up box
+where you can add or edit any source modifier. You can also import a
+source modifier table or export the existing source modifiers in table
+format from this page.
+
+#The Select Modifier dialog allows you to select a modifier from the
+pull-down list and edit the value of this modifier for each sequence or
+globally add a value to all sequences.
+
+#The two windows in this pop-up provide information about the current
+source modifiers for the sequences in your submission. The top window
+provides a summary of these modifiers and the lower window lists the
+values of each modifier for each sequence. If any sequences have
+missing organism names or have source information that is identical to
+another sequence, the SeqIDs will be shown in red in this window.
+Double-clicking on a modifier value in this window will launch a pop-up
+where you can edit this value. Double-clicking on the modifier name
+used in the header will launch a modifier-specific pop-up where you can
+globally edit the modifier value for all sequences or change the value
+for individual sequences.
+
+*Clear All Source Modifiers
+
+#This button will clear all modifiers previously entered in either the
+FASTA definition lines or the submission dialogs. This includes the
+organism name which is required for submission.
+
+>Protein Page
+
+#This page allows you to provide the protein sequence translated from
+the nucleotide sequence that you just entered. If the nucleotide
+sequence is alternatively spliced or contains multiple open reading
+frames, enter all of the protein sequences on this page. Each protein
+sequence will appear in the database record as a coding sequence (CDS)
+feature. Sequin will automatically determine which nucleotide
+sequences code for the protein and indicate the nucleotide sequence
+interval on the database record. Sequin also provides tools that allow
+you to view a graphical representation of all the open reading frames
+in your nucleotide sequence and to convert these reading frames into
+CDS features. These tools are described later in the help
+documentation under the
+
+<A HREF="#ORFFinder">
+ORF Finder.
+</A>
+
+*Conceptual Translation Confirmed by Peptide Sequencing
+
+#Most protein entries are computer-generated conceptual translations of
+a nucleic acid sequence. If you have confirmed this translation by
+direct sequencing either of the entire protein or of peptides derived
+from the protein, please check this box.
+
+*Incomplete at NH3 end/Incomplete at COOH end
+
+#If the sequence is lacking amino acids at the amino- or
+carboxy-terminal end of the protein, please check the appropriate box.
+
+*Create Initial mRNA with CDS Intervals
+
+#If you check this box, Sequin will make an mRNA feature with the same
+initial intervals (i.e., range of sequence) as the CDS feature. After
+the record has been assembled, you should edit the mRNA feature location
+to add the 5' UTR and 3' UTR intervals. This may be done either in the
+mRNA editor or in the sequence editor.
+
+*Import Protein FASTA
+
+#You can import a single or multiple protein sequences contained within
+a previously generated protein FASTA file.
+
+**FASTA Format for Protein Sequences
+
+#The basic FASTA format is the same as that used for
+<A HREF="#FASTAFormatforNucleotideSequences">
+nucleotide sequences
+</A>
+, with a FASTA definition line followed by the sequence itself.
+
+#In order to match the protein sequence to the correct nucleotide
+sequence, you must use the same Sequence Identifier (SeqID) that you
+used to identify the nucleotide sequence. Thus in cases of
+alternatively spliced genes, a single protein FASTA file can contain
+two unique sequences that have the same SeqID. Both coding regions
+will be added to the same nucleotide sequence.
+
+#The available modifiers for use in a protein FASTA definition line are
+different than those for a nucleotide FASTA definition line and are
+limited to information about the protein or gene itself and are
+contained within the examples below. The format remains [modifer=text].
+
+#Note in all cases, the FASTA definition line must not contain any hard
+returns. All information must be on a single line of text.
+
+#Examples of properly formatted protein FASTA definition lines are:
+
+<KBD><PRE>>Seq1 [protein=neuropilin 1] [gene=Nrp1]</KBD></PRE>
+
+<KBD><PRE>>ABCD [protein=merozoite surface protein 2] [gene=msp2] [protein_desc=MSP2]</KBD></PRE>
+
+<KBD><PRE>>DNA.new [protein=breast and ovarian cancer susceptibility protein] [gene=BRCA1] [note=breast cancer 1, early onset]</KBD></PRE>
+
+#The protein name should be included in the entry; all other fields are
+optional.
+
+#The line after the FASTA definition line begins the amino acid
+sequence. It is recommended that each line of sequence be no longer
+than 80 characters. Please only use IUPAC symbols within the amino
+acid sequence. Non-IUPAC amino acid symbols will be stripped from the
+sequence.
+
+#After you import your sequence, a window will appear with information
+about the sequence. The first line will describe the number of protein
+sequences imported and the total length in amino acids of
+all sequences. Each sequence is numbered, and its length,
+unique identifier (SeqID), Gene symbol, Protein name, and title
+(Definition line) as supplied in the FASTA definition line are listed.
+
+>Annotation Page
+
+#Note: This page will not be available if you have selected a segmented
+or gapped sequence as the
+<A HREF="#SubmissionType">
+Submission Type
+</A>
+.
+
+#On this page, you can add a
+<A HREF="#gene">
+gene
+</A>
+,
+<A HREF="#rRNA">
+ribosomal RNA
+</A>
+ or
+<A HREF="#CDS">
+CDS
+</A>
+ feature across the entire span of each sequence you are submitting.
+You can not specify locations within each sequence using this page.
+More options are available under the
+
+<A HREF="#AnnotateMenu">
+Annotate Menu
+</A>
+in the record viewer.
+
+#If the feature should be partial at one or both ends, check the
+appropriate box and then fill in the text boxes for the relevant
+feature.
+
+#You may add a title to all sequences if this was not included in the
+FASTA definition line. This will be used as the DEFINITION field in
+the final flatfile. The title should contain a brief description of
+the sequence. There is a preferred format for nucleotide and protein
+titles and Sequin can generate them automatically using the Generate
+Definition Line function under the Annotate menu in the record viewer.
+
+>Assembly Tracking
+
+#You will only see this form if you had previously indicated that the
+entry is a Third-Party Annotation submission. You must provide the
+GenBank Accession number(s) of the primary sequence used to assemble
+your TPA sequence. We can not accept primary sequences corresponding
+to Reference Sequences or those from proprietary databases. More
+information about this can be found on the
+
+<A HREF="http://www.ncbi.nlm.nih.gov/Genbank/tpa.html">
+TPA
+</A>
+home page.
+
+#If a proper GenBank Accession is entered in the first column of the
+Assembly Tracking form, the GenBank staff can map the coordinates for
+you. You do not need to fill out the 'from' and 'to' columns. Note
+that multiple accessions may be entered to provide full coverage of the
+assembled sequence.
+
+#You may also generate an Assembly Tracking form in the record viewer
+under the Annotate menu. Select Descriptors and TPA Assembly from the
+pull-down menu in order to generate the Assembly Tracking form.
+
+>Editing the Record
+
+*Overview
+
+#After you finish the Organism and Sequences Form, Sequin will process
+your entry based on the information you have entered. The window you
+see now is called the record viewer. This is also the window you will
+see if you are submitting an update to an existing record. The
+instructions after this point are the same whether you are submitting a
+new record or an update.
+
+#In the default window of the record viewer, you will see your entry
+approximately as it would appear in the database. Most of the
+information that you entered earlier in the submission process is
+present in the viewer; other information, such as the contact, is still
+present in the record but will not be visible in the database entry. If
+you have provided a conceptual translation of the nucleotide sequence,
+the translation will be listed as a CDS Feature. Sequin automatically
+determines which nucleotides encode for the protein, and lists them,
+even if the nucleotide sequence contains introns and exons.
+
+#You can save the entry to a file by selecting Save or Save As under the
+File menu. This is not the same as saving the entry for submission to
+the database. It is a good idea to save the file at this point so that
+if you make any unwanted changes during the editing process you can
+revert to the original copy. If you wish to edit the entry later, click
+on "Read Existing Record" on the Welcome to Sequin form and choose
+the file.
+
+#It is likely that the entry could be processed now for submission to
+the database. However, you may wish to add information to
+the entry. This information may be in the form of Descriptors or
+Features. Descriptors are annotations that apply to an
+entire sequence, or an entire set of sequences, and Features are
+annotations that apply to a specific sequence interval. For example,
+you may want to change the Reference Descriptor to add a published
+manuscript, or to annotate the sequence by adding features such as a
+signal peptide or polyA signal.
+
+#Information in the record viewer can be edited in different ways. One
+way to modify information is to double click within the block of
+information you wish to edit. Many blocks, such as "Definition",
+"Source", "Reference", or "Features" can be edited.
+
+#To add information, create a new descriptor
+or feature by selecting the appropriate form from the Misc or Features
+menus. These options are described later in this help document.
+
+#Finally, you may need to edit the sequence itself.
+<A HREF="#SequenceEditor">
+Instructions
+</A>
+for working with the sequence are presented in the documentation for the
+Sequence Editor.
+
+*Submitting the Finished Record to the Database
+
+#Once you are satisfied that you have added all the appropriate
+information, you must process your entry for submission to the database.
+ Select "Validate" under the Search menu. This function detects
+discrepancies between the format of your submission and that required by
+the database selected for entry.
+
+#If Sequin detects problems with the format of your record, you will see a
+screen listing the validation errors as well as suggestions for how to fix the
+discrepancies. Single clicking on an error message scrolls the record viewer
+to the feature that is causing the error. Double clicking on the error message
+launches a new form on which you can enter information to correct the problem.
+If you are annotating a set of multiple sequences, shift-click to scroll to the
+target sequence and feature. You can also dismiss the suggestion and proceed
+on your own. When you think you have corrected all the problems, click on
+"Revalidate".
+
+#Message: Select Verbose, Normal, Terse, or Table. Verbose gives a more
+detailed explanation of the problem.
+
+#Filter: Select the error messages you wish to see. You can select
+ALL, SEQ_INST (errors regarding the sequence itself, its type, or
+length), SEQ_DESCR (descriptor errors), SEQ_FEAT (feature errors), or
+errors specific to your record.
+
+#Severity: Select the types of error messages you wish to see. You
+will see the type of message selected, as well as any messages warning
+of more serious problems.
+
+#There are four types of error messages, Info, Warning, Error, and
+Reject. Info is the least severe, and Reject is the most severe. You
+may submit the record even if it does contain errors. However, we
+encourage you to fix as many problems as possible. Note that some
+messages may be merely suggestions, not discrepancies. A possible
+Warning message is that a splice site does not match the consensus.
+This may be a legitimate result, but you may wish to recheck the
+sequence. A possible Error message is that the conceptual translation
+of the sequence that you supplied does not encode an open reading
+frame. In this case, you should check that you translated the sequence
+in the correct reading frame. A possible Reject message is that you
+neglected to include the name of the organism from which the sequence
+was derived. The name of the organism is absolutely required for a
+database entry.
+
+#If Sequin does not detect any problems with the format of your record,
+you will see a message that "Validation test succeeded".
+
+#To prepare the submission, click the "Done" button on the record
+viewer, or select "Prepare Submission" under the File menu. You will be
+prompted to save the file. Email this file to the database at the
+address shown. You MUST email the file; Sequin does not submit the
+file automatically over the network. The email addresses for the
+databases are:
+
+!-GenBank: gb-sub@ncbi.nlm.nih.gov
+!-EMBL: datasubs@ebi.ac.uk
+!-DDBJ: ddbjsub@ddbj.nig.ac.jp
+
+#After your entry is complete, close the record viewer. You will be
+returned to the Welcome to Sequin form and can begin another entry.
+
+>The Record Viewer
+
+*Target Sequence
+
+#This pop-up menu shows a list of SeqIDs of all nucleotide and protein
+sequences associated with the Sequin entry. Use the menu to select the
+sequences displayed in the record viewer, as well as the sequences you
+want to "target", that is, the sequences to which you want to apply a
+descriptor (see
+<A HREF="#Descriptors">
+Descriptors
+</A>
+ in the Sequin help documentation). You may select either an individual
+sequence by name or a set of sequences, such as All Sequences, or
+SEG_dna if you have a segmented nucleotide set. You may change the
+selection at any time.
+
+*Display Format
+
+#You may change the display format of the record viewer to any of the
+formats described below. Editing a field in one display format will
+change that field in all formats. Subsequent pop-up menus will appear
+depending on which format is selected.
+
+**GenBank
+
+#This display format allows you to see the submission as it would appear
+as a GenBank or DDBJ entry. It is the default format.
+
+#The Mode pop-up default setting is Sequin. Release mode shows certain
+qualifiers and db_xrefs in RefSeq entries which are non-collaborative.
+Entrez mode is used fro web display and can show new elements that have
+not yet finished their four month quarentine period. Dump mode requires
+that the accession slot be populated. In most cases, there is no need
+to change from the default Sequin mode.
+
+#The Style pop-up allows different views of segmented records. The
+default is Normal. Segment style is the traditional representation of
+segmented sequences, while Contig style displays a CONTIG line with a
+join of accessions instead of raw sequence. Master style shows
+features mapped to the segmented sequence coordinates instead of the
+coordinates of the individual parts.
+
+**Graphic
+
+#This display format shows the entry in a graphical view. The top bar
+represents the nucleotide sequence. Lower arrows or bars represent
+different features on the sequence. Double click on an arrow or bar to
+launch the appropriate editing window. Any sequence highlighted in the
+Sequence Editor will be boxed on the graphical view of the sequence.
+To see a graphical representation of a segmented set (see
+
+<A HREF="#Submissiontype">
+Submission type
+</A>,
+above), the Target Sequence must be set to
+SEG_dna.
+
+#The Style pop-up menu allows you to see the display in different styles
+and colors.
+
+#The Scale pop-up menu allows you to see the display in different sizes.
+The smaller the number, the larger the display.
+
+**Sequence
+
+#This display format shows the nucleotide sequence in the record along
+with any annotated features (such as CDS or mRNA). You can only view a
+single sequence at a time with this option. You can use the Features
+pop-up menu to change the display of the features. With the numbering
+pop-up menu, select where you want the sequence numbers to be
+indicated, at the side of the sindow, at the top of each sequence line,
+or not at all.
+
+**Alignment
+
+#This display format shows sets of aligned sequences, such as those
+imported as part of a population, phylogenetic, mutation, or
+environmental samples set. When toggled to All Sequences in the Target
+Sequence pop-up, the alignment of all entries will be displayed. To
+more closely analyze similarities, you can select a single entry in the
+Target Sequence pop-up. The complete sequence of the entry selected
+will be displayed. Any nucleotides in the other sequences that differ
+from that selected will be displayed, while identical nucleotides will
+be displayed as a period. You can also display features annotated on
+the selected target sequence or all sequences using the Feature display
+toggle. To launch the alignment editor, select
+<A HREF="#AlignmentAssistant">
+Alignment Assistant
+</A>
+from the record viewer Edit menu.
+
+**EMBL
+
+#This display format allows you to see the submission as it would appear
+as an EMBL entry.
+
+**Table
+
+#This display format shows the annotation in a five-column, tab-delimited
+<A HREF="table.html">table</A>
+ format. This format can be imported to add annotation to a record that
+has none.
+
+**FASTA
+
+#This display shows the sequence and Definition line only, without any
+annotations, in a format called the FASTA format. This is a format used
+by many molecular biology analysis programs. You cannot edit in this
+display mode.
+
+**Quality
+
+#This display format shows quality score data ifit has been included in
+the submission.
+
+**ASN.1
+
+#This display shows the entry in Abstract Syntax Notation 1, a data
+description language used by the NCBI. You cannot edit in this display
+mode.
+
+**XML
+
+#This display format shows the entry in XML language, sometimes used by
+various databases. You cannot edit in this display mode.
+
+**INSDSeq
+
+#This display format shows the entry in the XML format used by the INSD.
+ You cannot edit in this display mode.
+
+**Desktop
+
+#The NCBI DeskTop displays the internal
+structure of the record being viewed in Sequin. The
+<A HREF="#NCBIDeskTop">
+DeskTop
+</A>
+is explained under the Misc menu.
+
+*Done
+
+#This button allows you to validate the entry when you are finished with
+the submission. See
+<A HREF="#SubmittingtheFinishedRecordtotheDatabase">
+Submitting the Finished Record to the Database
+</A>
+ in the Sequin help documentation.
+
+*Controls for Downloaded Entries
+
+#If you have downloaded a sequence from Entrez, you will see an
+additional button labeled PubMed. This button will launch a web
+browser containing the target sequence as it appears in Entrez. From
+here, you can access any Entrez-supported Links, including related
+sequences and associated references in PubMed.
+
+>Descriptors
+
+*Overview
+
+#Descriptors are annotations that apply to an entire sequence, or an
+entire set of sequences, in a given entry. They do not have a specific
+location on a sequence, as they apply to the entire sequence. They can
+be contrasted to
+<A HREF="#Features">
+Features,
+</A>
+which apply to a specific interval of the sequence.
+
+#You may edit descriptors in one of two ways.
+
+#(1) In the record viewer, double click within the text of the
+descriptor to bring up a form on which information can be added.
+
+#(2) Choose the option Descriptors from the Annotate menu.
+
+*Annotate Menu
+
+#This menu allows you either to create new descriptors or to modify
+existing ones. Select the descriptor that you wish to modify.
+
+#When you first select a descriptor, you will see a window called
+"Descriptor Target Control". Using the target control pop-up menu,
+select the sequences you wish this descriptor to cover. The name(s)
+listed correspond to the SeqID(s) given to the nucleotide or amino acid
+sequences when when they were imported into Sequin. The default
+selection for this menu is set in the Target Sequence pop-up menu on
+the record viewer. You may choose to have the descriptor cover just
+one sequence, or a set of sequences in your entry. If you are creating
+a new descriptor, select "Create New". If you wish to modify a
+previous descriptor, select "Edit Old".
+
+#The following is a list of some of the descriptors that can be added.
+Two additional descriptors, those for
+<A HREF="#Publications">
+Publications
+</A>
+and
+<A HREF="#BiologicalSourceDescriptororFeature">
+Biological Source,
+</A>
+are described in other sections.
+
+**TPA Assembly
+
+#If you indicated that your sequence is a TPA submission, a
+<A HREF="#AssemblyTracking">
+TPA Assembly
+</A>
+ was created from the information regarding primary accession numbers.
+This Assembly information can be edited here. Note that it is not
+necessary to enter nucleotide location in the "from" and "to" columns.
+
+**Update Date
+
+#This is for database staff use only. Please do not modify the date.
+
+**Create Date
+
+#This is for database staff use only. Please do not modify the date.
+
+**Region
+
+#This descriptor provides general information about the genetic context
+of the sequence. For example, if your nucleotide sequence is cloned
+from the region surrounding the Huntington's Disease gene, you could
+enter that information here. Providing information for this descriptor
+is optional.
+
+**Name
+
+#Alternative place for a descriptive name for the sequence. This
+information will not appear in the flatfile view, but will be
+maintained in the ASN1.
+
+**Comment
+
+#This descriptor is used to list any additional information that you
+wish to provide about the sequence. Use of this descriptor is optional.
+ Most information can be better annotated using the appropriate
+features and qualifiers rather than a generic comment descriptor.
+
+**Title
+
+#This descriptor contains the information that will go on the Definition
+line of the database entry. If you supplied a title for your
+nucleotide sequence when you imported it into Sequin, that information
+is here. If you wish to change the Definition line, or if you did not
+supply a title when you submitted the sequence, edit this Descriptor.
+For more information on creating proper Definition lines, please see
+the Sequin help documentation for the
+
+<A HREF="#NucleotideDefinitionLine(Title)">
+Nucleotide Definition Line (Title)
+</A>.
+
+**Molecule Description
+
+#This descriptor indicates the characteristics of the molecule from
+which the sequence was derived. The information that you have already
+entered can be edited here. In most cases, the molecule and class are
+the only choices which should be edited from the default values.
+
+***Molecule
+
+#A GenBank sequence can represent one of several different molecule
+types. Enter in the Molecule pop-up menu the type of molecule that was
+sequenced. A brief description of the choices in this pop-up menu were
+listed previously.
+
+***Completedness
+
+Choose the appropriate option from the pop-up menu.
+
+#-Complete: Use this designation when a complete molecule, such as a
+complete mitochondrial genome, is being submitted.
+
+#-Partial: Use this designation when an incomplete unit, such as the
+partial coding sequence of a gene, is being submitted.
+
+#-No left: Use this designation when an incomplete unit, such as the
+partial coding sequence of a gene, or a partial protein sequence, is
+being submitted. The sequence has no left if it is incomplete on the
+5', or amino-terminal, end.
+
+#-No right: Use this designation when an incomplete unit, such as the
+partial coding sequence of a gene, or a partial protein sequence, is
+being submitted. The sequence has no right if it is incomplete on the
+3', or carboxy-terminal, end.
+
+#-No ends: Use this designation when an incomplete unit, such as the
+partial coding sequence of a gene, or a partial protein sequence, is
+being submitted, The sequence has no ends if it is incomplete at both
+the 5' and 3', or amino- and carboxy- terminal, ends.
+
+#-Other: Use this designation when none of the above descriptions apply.
+
+***Technique
+
+#From the pop-up menu, select the technique that was used to generate the
+sequence.
+
+#-Standard: standard sequencing technique.
+
+#-EST:
+<A HREF="http://www.ncbi.nlm.nih.gov/dbEST/index.html">
+Expressed Sequence Tag
+</A>
+: single-pass, low-quality mRNA sequences
+derived from cDNAs. These sequences will appear in the EST division.
+
+#-STS:
+<A HREF="http://www.ncbi.nlm.nih.gov/dbSTS/index.html">
+ Sequence Tagged Site
+</A>
+: short sequences that are operationally
+unique in a genome and that define a specific position on the physical
+map. These sequences will appear in the STS division.
+
+#-Survey:
+<A HREF="http://www.ncbi.nlm.nih.gov/dbGSS/index.html">
+single-pass genomic sequence
+</A>
+. These sequences will appear in
+the Genome Survey Sequence (GSS) division.
+
+#-Genetic Map: Genetic map information, for example, in the Genomes division.
+
+#-Physical Map: Physical map information, for example in the Genomes division.
+
+#-Derived: A sequence assembled into a contig from shorter sequences.
+
+#-Concept-trans: A protein translation generated with the appropriate
+genetic code.
+
+#-Seq-pept: Protein sequence was generated by direct sequencing of a
+peptide.
+
+#-Both: Protein sequence was generated by conceptual translation and
+confirmed by peptide sequencing.
+
+#-Seq-pept-Overlap: Protein sequence was generated by sequencing
+multiple peptides, and the order of peptides was determined by overlap
+in their sequences.
+
+#-Seq-pept-Homol: Protein sequence was generated by sequencing
+multiple peptides, and the order of peptides was determined by homology
+with another protein.
+
+#-Concept-Trans-A: Conceptual translation of the nucleotide sequence
+provided by the author of the entry.
+
+#-HTGS 0:
+<A HREF="http://www.ncbi.nlm.nih.gov/HTGS/">
+High Throughput Genome Sequence
+</A>
+, Phase 0. These sequences
+are produced by high-throughput sequencing projects and will be in the
+HTG division.
+
+#-HTGS 1:
+<A HREF="http://www.ncbi.nlm.nih.gov/HTGS/">
+High Throughput Genome Sequence
+</A>
+, Phase 1. These sequences
+are produced by high-throughput sequencing projects and will be in the
+HTG division.
+
+#-HTGS 2:
+<A HREF="http://www.ncbi.nlm.nih.gov/HTGS/">
+High Throughput Genome Sequence
+</A>
+, Phase 2. These sequences
+are produced by high-throughput sequencing projects and will be in the
+HTG division.
+
+#-HTGS 3:
+<A HREF="http://www.ncbi.nlm.nih.gov/HTGS/">
+High Throughput Genome Sequence
+</A>
+, Phase 3. These sequences
+are produced by high-throughput sequencing projects and will be in the
+HTG division.
+
+#-FLI_cDNA: Full Length Insert cDNA. Sequence corresponds to entire cDNA but
+not necessarily entire transcript. These sequences are produced by large
+sequencing projects.
+
+#-HTC: High Throughput cDNA. These sequences are produced by large sequencing
+projects.
+
+#-WGS:
+<A HREF="http://www.ncbi.nlm.nih.gov/Genbank/wgs.html">
+Whole Genome Shotgun
+</A>
+. These sequences are produced by large sequencing projets and follow a
+separate submission process.
+
+#-Barcode: Nucleotide sequence is part of Barcodes of Life project. This
+selection should only be used by members of the Consortium for the
+Barcodes of Life.
+
+#-Other: Do not use this designation.
+
+***Class
+
+#From the pop-up menu, select the type of molecule that was sequenced.
+
+#-DNA: DNA
+
+#-RNA: RNA
+
+#-Protein: Protein
+
+#-Nucleotide: Do not select this item
+
+#-Other: Do not select this item
+
+***Topology
+
+#From the pop-up menu, select the topology of the sequenced molecule.
+
+#-Linear: Linear molecule (most sequences).
+
+#-Circular: Circular molecule (such as a complete plasmid or mitochondrion).
+
+#-Tandem: Do not select this item.
+
+#-Other: Do not select this item.
+
+***Strand
+
+#From the pop-up menu, select whether the sequence was derived from an
+organism with a single- or double-stranded genome. This is used primarily for
+viral submissions.
+
+#-Single: The organism contains only a single-stranded genome, for
+example, ssRNA viruses.
+
+#-Double: The organism contains only a double-stranded genome, for
+example, dsDNA viruses.
+
+#-Mixed: Do not select this item.
+
+#-Mixed Rev: Do not select this item.
+
+#-Other: Do not select this item.
+
+**Biological Source
+
+#The Biological Source descriptor is described in more detail
+<A HREF="#BiologicalSourceDescriptororFeature">
+below.
+</A>
+
+>Features
+
+*Overview
+
+#Features are annotations which apply to one or more intervals on a
+sequence. They can be contrasted to
+<A HREF="#Descriptors">
+Descriptors,
+</A>
+that apply to an entire sequence or an entire set of sequences.
+Features will be added to the Target Sequence selected in the record
+viewer pop-up menu.
+
+#You may add or modify features in one of three ways.
+
+#(1) In the record viewer, double click on the text of an existing
+feature to bring up a form on which information can be added or edited.
+
+#(2) Choose the feature from the Annotate menu to add a new feature.
+
+#(3) Choose the feature from the Sequence Editor Features menu to add a
+new feature.
+
+#The features listed in the Annotate menu and the Sequence Editor
+Features menu are identical, and the instructions for adding them are
+the same, with one exception. If you annotate them in the Annotate
+menu, you must provide the nucleotide sequence location of the feature.
+ However, if you add features from the Sequence Editor, you can
+highlight the sequence that the feature covers, and the location of the
+sequence will be automatically entered in the feature location box.
+
+*Annotate Menu
+
+#This menu allows you to add or modify features on the sequence selected
+in the Target Sequence pop-up menu of the record viewer. Features are
+grouped into six categories. Select the feature that you would like to
+mark on your sequence. A new form will appear.
+
+#Feature forms share a common design. The first page is specific to the
+particular feature, e.g., Coding Region or Gene. The second page lists
+Properties of the Feature. The third page describes the Location of the
+feature. Details about the common second and third pages are provided
+below.
+
+**Properties Page
+
+***General Subpage
+
+#Enter general comments about the feature here.
+
+#Select any of the flags if necessary. If this sequence contains only a
+partial representation of the feature you are describing, check the
+"Partial" box. Check the "Exception" box if the feature annotates a
+post-transcriptional modification of the nucleotide sequence, such as
+ribosomal slippage or RNA editing. This is generally used only on CDS
+features. The evidence dialogs will only be editable if information
+has been entered in the Evidence subpage.
+
+#If a gene feature overlaps the feature you are editing, the gene symbol
+will appear in the pull-down menu. If you want to add the name of a
+new gene, select new, and enter its name and optional description. By
+default, mapping between the feature and the gene is done by overlap,
+that is, the gene associated with the feature is the gene whose
+location overlaps with the location of the feature. Under some
+circumstances, for example, if the sequences of two genes overlap, you
+may wish the feature to apply to a different gene. In this case,
+select cross-reference, and select the name of the new gene in the
+pop-up menu. If you do not want the feature to map to any existing
+gene, select suppress. You may also edit information on the Gene
+feature form by clicking on Edit Gene Feature.
+
+***Comment Subpage
+
+#Add any comments about the feature here, especially if you checked the
+"Exception" box on the General Subpage.
+
+***Citations Subpage
+
+#This page is used to list any citations that specifically apply to the
+feature you are annotating. The citation must have already been entered
+into the record (see
+<A HREF="#Publications">
+Publications
+</A>)
+ in the Sequin help documentation. Click on Edit Citations, and
+place a check mark in box next to the publication you want to cite.
+However, we discourage the use of citations on features.
+
+***Cross-Refs Subpage
+
+#This is a read-only page used to cross-reference this entry to entries
+in external databases (databases other than GenBank, EMBL/EBI, and
+DDBJ), such as dbEST or FLYBASE. For more information on this topic,
+see the International Nucleotide Sequence Database Collaboration
+
+<A HREF="http://www.ncbi.nlm.nih.gov/collab/db_xref.html">
+page
+</A>.
+http://www.ncbi.nlm.nih.gov/collab/db_xref.html
+
+***Evidence Subpage
+
+#This page is primarily used by large sequencing centers to explain
+annotation prediction methods and its use is optional. More details
+about these qualifiers can be found in the
+<A HREF="http://www.ncbi.nlm.nih.gov/GenBank/evidence.html">
+genome submission guidelines
+</A>.
+The two choices of evidence are Experiment or Inference.
+
+#Wet-bench, experimental evidence can be entered as free text in the
+Experiment section. Please be as brief as possible.
+
+#The Inference section allows for information to be added in cases where
+the feature is annotated based solely on sequence similarity or
+prediction software. In order to fill in text, you must select one of
+the options from the Category pull-down menu. Different pull-down and
+text boxes will appear depending on the selection you choose from the
+Category menu. If you select one of the 'similar to' categories, you
+must include the name of the database and the corresponding accession
+number of the sequence used as the basis for the annotation. If you
+choose one of the prediction categories, you must include the name and
+version of the prediction program used as the basis for the annotation.
+
+#For example, if your annotation of a coding region was based on
+similarity to the sequence and annotation in GenBank Accession number
+AY411252, you would select "similar to DNA sequence" from the pull-down
+menu and then select "INSD" in the Database pull-down. You would then
+type "AY411252.1" in the Accession text box. If the annotation is
+based on the Genscan prediction algorithm, you would select "ab initio
+prediction" from the pull-down menu, select "Genscan" in the Program
+pull-down and enter 2.0 in the Program Version text box. If the
+database or program used is not listed in the appropriate pull-down
+list, select Other from the list. A new text box will appear where you
+can enter the name of the database or program used. You still must
+include the appropriate accession number or version in the subsequent
+text box.
+
+***Identifiers Subpage
+
+#This is a read-only page used by the database staff for tracking
+features within the record.
+
+**Location Page
+
+#This page allows you to select the location of the feature you are
+citing. Each feature must have a sequence interval associated with it.
+In most cases, Sequin will limit the option to the nucleic acid or
+protein sequence as appropriate.
+
+#Check the 5' Partial or 3' Partial box if the feature in your nucleic
+acid sequence is missing residues at the 5' or 3' ends, respectively.
+Check the NH2 Partial or COOH Partial if the feature in your amino acid
+sequence is missing residues at the amino- or carboxy-terminal ends,
+respectively. If you checked "Partial" on the Properties page, you
+must check either the 5' and/or 3' partial boxes.
+
+#Enter the sequence range of the feature. The numbers should correspond
+to the nucleotide sequence interval if the SeqID is set to a nucleotide
+sequence, and to an amino acid sequence interval if the SeqID is set to
+a protein sequence. If the feature spans multiple, non-continuous
+intervals on the sequence, indicate the beginning and end points of each
+interval. If each interval is separate, and should not be joined with
+the others to describe the feature, check the Intersperse intervals with
+gaps box (for example, when annotating multiple primer binding sites).
+If the feature is composed of several intervals that should all be
+joined together, do not check the box (for example, when annotating mRNA
+on a genomic DNA sequence).
+
+#For nucleic acid Features only: From the pop-up menu, select the
+strand on which the feature is found.
+
+#-Plus: Plus strand, or coding strand.
+
+#-Minus: Minus strand, or non-coding strand.
+
+#-Both: Both strands.
+
+#-Reverse: Do not select this item.
+
+#-Other: Do not select this item.
+
+#Use the pop-up menu to select the SeqID of the sequence you are
+describing by the location.
+
+#If you are working on a set of sequences which contain an alignment,
+you will see a toggle at the bottom of the Location Page where you can
+select to add or view the location of the feature using the Sequence
+Coordinates of the target sequence or the Alignment Coordinates. In
+either case, the feature will only be added to the target sequence. If
+you want to add features to all members of the set using the alignment
+coordinates, you must use the
+
+<A HREF="http://www.ncbi.nlm.nih.gov/Sequin/sequin.hlp.html#Workingwithsetsofalignedsequences">
+Alignment Assistant
+</A>
+.
+#A brief description of the available features follows. A detailed
+explanation of how to use the coding region (CDS) feature is included.
+The DDBJ/EMBL/GenBank feature table definition
+<A HREF="http://www.ncbi.nlm.nih.gov/collab/FT/index.html">
+page
+</A>
+http://www.ncbi.nlm.nih.gov/collab/FT/index.html
+ provides detailed information about other features.
+
+*attenuator
+
+#1) region of DNA at which regulation of termination of transcription
+occurs, which controls the expression of some bacterial operons; 2)
+sequence segment located between the promoter and the first structural
+gene that causes partial termination of transcription.
+
+*C_region
+
+#Constant region of immunoglobulin light and heavy chains, and T-cell
+receptor alpha, beta, and gamma chains. Includes one or more exons,
+depending on the particular chain.
+
+*CAAT_signal
+
+#CAAT box; part of a conserved sequence located about 75 bp upstream of
+the start point of eukaryotic transcription units that may be involved
+in RNA polymerase binding; consensus=GG(C or T)CAATCT.
+
+*CDS
+
+#coding sequence; sequence of nucleotides that corresponds with the
+sequence of amino acids in a protein (location includes stop codon).
+Feature includes amino acid conceptual translation.
+
+**Coding Region Page
+
+#Most users add a coding region to their sequence when they fill out the
+Organism and Sequences form. However, you may need to edit the coding
+region, or add additional ones. Choose CDS under the Coding Regions
+and Transcripts submenu of the Features menu, or to edit an existing
+CDS, double click on the record viewer. If you appended the partial
+sequence of a coding region to the Organism and Sequences form, you will
+probably need to edit the Coding Region feature to avoid validation
+error messages about the location of the coding region.
+
+***General (Product) Subpage
+
+#Choose the genetic code that should be used to translate the
+nucleotide sequence. For more information, and for the translation
+tables themselves, see the NCBI Taxonomy
+<A HREF="http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c">
+page
+</A>.
+If the genetic code is already populated from the taxonomy database, do
+not change this selection.
+
+#Choose the reading frame in which to translate the sequence. Do not
+fill in the Protein Product or SeqID selections.
+
+#Supply additional information about the protein by clicking on Edit
+Protein Information to launch the Protein feature forms. The protein
+name must have already been filled out on the Protein subpage.
+
+#Checking retranslate on accept will translate the nucleotide sequence
+according to the interval(s) indicated on the Locations page when you
+click on Accept to exit the editor. This new translation will replace
+any earlier translations you have supplied. This should not be a
+problem if the interval was indicated appropriately.
+
+#If the coding sequence that you supply is a partial sequence and you
+have checked a Partial box on the Location subpage, it is a good idea to
+check the Synchronize Partials box. In this case, Sequin will ensure
+that all other appropriate features (such as protein) are also marked as
+partial.
+
+#When editing existing CDS features, choose the sequence you want to
+view by selecting its name uder the Product pop-up menu. You may also
+import a new protein sequence by selecting Import Protein FASTA under
+the file menu. The sequence should be formatted as described above on
+the Organism and Sequences form.
+
+#After you have imported a protein sequence, click on Predict Interval.
+This function will predict the interval on the nucleotide sequence to
+which the coding region applies. If you do not select this function,
+the interval will likely be wrong, and you will get an error message
+when you attempt to validate the record. If your sequence is a 5' or 3'
+partial, you must first indicate this manually on the Location Page.
+
+#You may also have Sequin generate the protein sequence from the
+nucleotide sequence by clicking on Translate Product. However, you must
+first indicate the location and partialness of the coding region on the
+Location page in order to obtain the correct translation.
+
+***Protein Subpage
+
+#Use this page to enter or edit a name or descriptionof the protein
+product. For a new sequence, enter information directly into the
+boxes. You can edit descriptions of an existing sequence by clicking
+on Edit Protein Feature which will bring up the Protein feature form.
+The Launch Product Viewer displays the flatfile view of ht eprotein
+record generated from the information in the CDS feature.
+
+***Exceptions Subpage
+
+#Exceptions describe places where there is a posttranslational
+modification. Enter the amino acid position at which the modification
+occurs, and select the amino acid that is actually represented in the
+protein from the pop-up list. Sequin will change the amino acid number
+to a nucleotide interval. Please provide some explanation for the
+exception in a comment.
+
+*conflict
+
+#Independent determinations of the "same" sequence differ at this site
+or region.
+
+*D-loop
+
+#Displacement loop; a region within mitochondrial DNA in which a short
+stretch of RNA is paired with one strand of DNA, displacing the
+original partner DNA strand in this region; also used to describe the
+displacement of a region of one strand of duplex DNA by a single
+stranded invader in the reaction catalyzed by RecA protein.
+
+*D_segment
+
+#Diversity segment of immunoglobulin heavy chain, and T-cell receptor
+beta chain.
+
+*enhancer
+
+#A cis-acting sequence that increases the utilization of (some)
+eukaryotic promoters and can function in either orientation and in any
+location (upstream or downstream) relative to the promoter.
+
+*exon
+
+#Region of genome that codes for portion of spliced mRNA; may contain
+5' UTR, all CDSs, and 3' UTR.
+
+*gap
+
+#Gap in the sequence, only applied to gaps of unknown length. The
+location span of the gap feature is 100 base pairs, indicated by 100 "n"s
+in the sequence. The qualifier /estimated_length=unknown is mandatory.
+
+*GC_signal
+
+#GC box; a conserved GC-rich region located upstream of the start point
+of eukaryotic transcription units that may occur in multiple copies or
+in either orientation; consensus=GGGCGG.
+
+*gene
+
+#Region of biological interest identified as a gene and for which a name
+has been assigned.
+
+*iDNA
+
+#Intervening DNA; DNA which is eliminated through any of several kinds
+of recombination.
+
+*intron
+
+#A segment of DNA that is transcribed, but removed from within the
+transcript, by splicing together the sequences (exons) on either side of
+it.
+
+*J_segment
+
+#Joining segment of immunoglobulin light and heavy chains, and T-cell
+receptor alpha, beta, and gamma chains.
+
+*LTR
+
+#Long terminal repeat, a sequence directly repeated at both ends of a
+defined sequence, of the sort typically found in retroviruses.
+
+*mat_peptide
+
+#Mature peptide or protein coding sequence; coding sequence for the
+mature or final peptide or protein product following post-translational
+modification. The location does not include the stop codon (unlike the
+corresponding CDS).
+
+*misc_binding
+
+#Site in nucleic acid that covalently or non-covalently binds another
+moiety that cannot be described by any other Binding key (primer_bind or
+protein_bind).
+
+*misc_difference
+
+#Feature sequence is different from that presented in the entry and
+cannot be described by any other Difference key (conflict, unsure,
+old_sequence, mutation, variation, allele, or modified_base).
+
+*misc_feature
+
+#Region of biological interest which cannot be described by any other
+feature key.
+
+*misc_recomb
+
+#Site of any generalized, site-specific, or replicative recombination
+event where there is a breakage and reunion of duplex DNA that cannot be
+described by other recombination keys (iDNA and virion) or qualifiers of
+source key (/insertion_seq, /transposon, /proviral).
+
+*misc_RNA
+
+#Any transcript or RNA product that cannot be defined by other RNA keys
+(prim_transcript, precursor_RNA, mRNA, 5'clip, 3'clip, 5'UTR, 3'UTR,
+exon, intron, polyA_site, rRNA, tRNA, scRNA, snoRNA, and snRNA).
+
+*misc_signal
+
+#Any region containing a signal controlling or altering gene function or
+expression that cannot be described by other Signal keys (promoter,
+CAAT_signal, TATA_signal, -35_signal, -10_signal, GC_signal, RBS,
+polyA_signal, enhancer, attenuator, terminator, and rep_origin).
+
+*misc_structure
+
+#Any secondary or tertiary structure or conformation that cannot be
+described by other Structure keys (stem_loop and D-loop).
+
+*modified_base
+
+#The indicated nucleotide is a modified nucleotide and should be
+substituted for by the indicated molecule (given in the mod_base
+qualifier value).
+
+*mRNA
+
+#messenger RNA; includes 5' untranslated region (5' UTR), coding sequences
+(CDS, exon) and 3' untranslated region (3' UTR).
+
+*N_region
+
+#Extra nucleotides inserted between rearranged immunoglobulin segments.
+
+*old_sequence
+
+#The presented sequence revises a previous version of the sequence at
+this location.
+
+*operon
+
+#Region containing polycistronic transcript under the control of the same
+regulatory sequences.
+
+*oriT
+
+Origin of transfer; region of DNA where transfer is initiated during the
+process of conjugation or mobilization.
+
+*polyA_signal
+
+#Recognition region necessary for endonuclease cleavage of an RNA
+transcript that is followed by polyadenylation; consensus=AATAAA.
+
+*polyA_site
+
+#Site on an RNA transcript to which will be added adenine residues by
+post-transcriptional polyadenylation.
+
+*precursor_RNA
+
+#Any RNA species that is not yet the mature RNA product; may include 5'
+clipped region (5' clip), 5' untranslated region (5' UTR), coding
+sequences (CDS, exon), intervening sequences (intron), 3' untranslated
+region (3' UTR), and 3' clipped region (3' clip).
+
+*prim_transcript
+
+#Primary (initial, unprocessed) transcript; includes 5' clipped region
+(5' clip), 5' untranslated region (5' UTR), coding sequences (CDS, exon),
+intervening sequences (intron), 3' untranslated region (3' UTR), and 3'
+clipped region (3' clip).
+
+*primer_bind
+
+#Non-covalent primer binding site for initiation of replication,
+transcription, or reverse transcription. Includes site(s) for synthetic
+e.g., PCR primer elements.
+
+*promoter
+
+#Region on a DNA molecule involved in RNA polymerase binding to initiate
+transcription.
+
+*protein_bind
+
+#Non-covalent protein binding site on nucleic acid.
+
+*RBS
+
+#Ribosome binding site.
+
+*repeat_region
+
+#Region of genome containing repeating units.
+
+*repeat_unit
+
+#Single repeat element.
+
+*rep_origin
+
+#Origin of replication; starting site for duplication of nucleic acid to
+give two identical copies.
+
+*rRNA
+
+#Mature ribosomal RNA ; the RNA component of the ribonucleoprotein
+particle (ribosome) that assembles amino acids into proteins.
+
+*S_region
+
+#Switch region of immunoglobulin heavy chains. Involved in the
+rearrangement of heavy chain DNA leading to the expression of a
+different immunoglobulin class from the same B-cell.
+
+*satellite
+
+#Many tandem repeats (identical or related) of a short basic repeating
+unit; many have a base composition or other property different from the
+genome average that allows them to be separated from the bulk (main
+band) genomic DNA.
+
+*scRNA
+
+#Small cytoplasmic RNA; any one of several small cytoplasmic RNA
+molecules present in the cytoplasm and (sometimes) nucleus of a
+eukaryote.
+
+*sig_peptide
+
+#Signal peptide coding sequence; coding sequence for an N-terminal
+domain of a secreted protein; this domain is involved in attaching
+nascent polypeptide to the membrane; leader sequence.
+
+*snRNA
+
+#Small nuclear RNA involved in pre-mRNA splicing and processing.
+
+*snoRNA
+
+#Small nucleolar RNA molecules generally involved in rRNA modification
+and processing.
+
+*source
+
+#Identifies the biological source of the specified span of the sequence.
+This key is mandatory. Every entry will have, as a minimum, a single
+source key spanning the entire sequence. More than one source key per
+sequence is permittable.
+
+*stem_loop
+
+#Hairpin; a double-helical region formed by base-pairing between
+adjacent (inverted) complementary sequences in a single strand of RNA or
+DNA.
+
+*STS
+
+#Sequence Tagged Site. Short, single-copy DNA sequence that
+characterizes a mapping landmark on the genome and can be detected by
+PCR. A region of the genome can be mapped by determining the order of a
+series of STSs.
+
+*TATA_signal
+
+#TATA box; Goldberg-Hogness box; a conserved AT-rich septamer found
+about 25 bp before the start point of each eukaryotic RNA polymerase II
+transcript unit that may be involved in positioning the enzyme for
+correct initiation; consensus=TATA(A or T)A(A or T).
+
+*terminator
+
+#Sequence of DNA located either at the end of the transcript or adjacent
+to a promoter region that causes RNA polymerase to terminate
+transcription; may also be site of binding of repressor protein.
+
+*transit_peptide
+
+#Transit peptide coding sequence; coding sequence for an N-terminal
+domain of a nuclear-encoded organellar protein; this domain is involved
+in post- translational import of the protein into the organelle.
+
+*tRNA
+
+#Mature transfer RNA, a small RNA molecule (75-85 bases long) that
+mediates the translation of a nucleic acid sequence into an amino acid
+sequence.
+
+*unsure
+
+#Author is unsure of exact sequence in this region.
+
+*V_region
+
+#Variable region of immunoglobulin light and heavy chains, and T-cell
+receptor alpha, beta, and gamma chains. Codes for the variable amino
+terminal portion. Can be made up from V_segments, D_segments,
+N_regions, and J_segments.
+
+*V_segment
+
+#Variable segment of immunoglobulin light and heavy chains, and T-cell
+receptor alpha, beta, and gamma chains. Codes for most of the variable
+region (V_region) and the last few amino acids of the leader peptide.
+
+*variation
+
+#A related strain contains stable mutations from the same gene (e.g.,
+RFLPs, polymorphisms, etc.) that differ from the presented sequence at
+this location (and possibly others).
+
+*3'clip
+
+#3'-most region of a precursor transcript that is clipped off during
+processing.
+
+*3'UTR
+
+#Region near or at the 3' end of a mature transcript (usually following
+the stop codon) that is not translated into a protein; trailer.
+
+*5'clip
+
+#5'-most region of a precursor transcript that is clipped off during
+processing.
+
+*5'UTR
+
+#Region near or at the 5' end of a mature transcript (usually preceding
+the initiation codon) that is not translated into a protein; leader.
+
+* -10_signal
+
+#Pribnow box; a conserved region about 10 bp upstream of the start point
+of bacterial transcription units that may be involved in binding RNA
+polymerase; consensus=TAtAaT.
+
+* -35_signal
+
+#A conserved hexamer about 35 bp upstream of the start point of
+bacterial transcription units; consensus = TTGACa or TGTTGACA.
+
+>Biological Source Descriptor or Feature
+
+#This annotation is very important, as an entry cannot be processed by
+the databases unless it includes some basic information about the
+organism from which the sequence was derived. This basic information was
+entered previously in the submission, in the Organism and Sequences
+Form. The more detailed Organism Information form allows you to alter
+or add to the data you entered earlier.
+
+*Overview: Descriptor or Feature?
+
+#Sequin allows two types of biological source information to be entered,
+Biological Source Descriptors and Biological Source Features. Biological
+Source Descriptors, like other descriptors, provide organism information
+about an entire sequence, or an entire set of sequences, in an entry.
+Biological Source Features, like other features, provide organism
+information about a specific interval on a given sequence.
+
+#In most cases, you will want to use a Biological Source Descriptor, because
+all the sequences in the entry will derive from the same source.
+However, if you have sequenced a transgenic molecule, for example, one
+that is part plant and part bacterial, you would use Biological Source
+Features to annotate which sequence was derived from plant and which from
+bacteria.
+
+#To add a Biological Source Descriptor, select Biological Source under
+the Descriptor section of the Annotate menu. To add a Biological
+Source Feature, select Biological Source under the Bibliographic and
+Comments section of the Annotate menu.
+
+#Annotating a Biological Source Descriptor or Feature is similar to
+annotating any descriptor or feature. For help in creating descriptors
+and features, see the appropriate section of the help documentation.
+The following are instructions for filling out Biological
+Source-specific forms.
+
+*Organism Page
+
+**Names Subpage
+
+#The scrollable list contains the scientific names of many organisms.
+To reach a name on the list, either type the first few letters of the
+scientific name, or use the thumb bar. Click on a name from the list to
+fill out the scientific name field. If there is a common name for the
+organism, that field will be filled out automatically. You may also
+directly type in the scientific name. If you have any questions about
+the scientific or common name of an organism, see the NCBI
+<A HREF="http://www.ncbi.nlm.nih.gov/Taxonomy/tax.html">
+taxonomy browser
+</A>
+http://www.ncbi.nlm.nih.gov/Taxonomy/tax.html
+
+**Location Subpage
+
+***Location of Sequence
+
+#From the selection list, please enter the location of the genome that
+contains your sequence. Most entries will have a "Genomic" location.
+A brief description of the choices in this pop-up menu were listed
+previously.
+
+***Origin of Sequence
+
+#This menu is for the use of database personnel. Please leave this
+field empty. The Biological focus box should be checked in rare cases
+where multiple source features are annotated.
+
+**Genetic Codes Subpage
+
+#Please use these fields to select the nuclear and mitochondrial genetic
+code that should be used to translate the nucleic acid sequence. The
+genetic code for a eukaryotic organism is "Standard". If you selected
+an organism name from the scrollable list described above, this field
+was filled out automatically. Do not change these fields if they have
+been filled out automatically.
+
+#For more information regarding the translation tables available, see
+the NCBI Taxonomy
+
+<A HREF="http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c">
+page
+</A>.
+
+**Lineage Subpage
+
+#This information is normally entered by the database staff. They will
+use the
+<A HREF="http://www.ncbi.nlm.nih.gov/Taxonomy/tax.html">
+Taxonomy database
+http://www.ncbi.nlm.nih.gov/Taxonomy/tax.html
+</A>
+ maintained by the NCBI/GenBank.
+
+#If you disagree with the lineage supplied please notify the database
+staff.
+
+#If you are running Sequin in its
+<A HREF="#NetConfigure">
+network-aware
+</A>
+mode, you will see a button labeled "Lookup Taxonomy". Click on this
+button to perform an automatic look-up of the taxonomic lineage of the
+organism. Sequin will perform the look-up by accessing the Taxonomy
+database and will fill out the Taxonomic Lineage and
+Division fields.
+
+#If you have any comments about the taxonomic lineage determined by
+Sequin, please submit these comments with your entry. Under the Sequin
+File menu, select Edit Submitter Info. Enter your comments in the box
+entitled "Special Instructions to Database Staff", on the Submission
+page.
+
+*Modifiers Page
+
+#This page allows you to enter additional information about the source
+and/or organism. Entering information is optional.
+
+**Source Subpage
+
+#Choose a modifier from the pull-down menu on the left side of the page
+and type the appropriate name on the right side of the page. If you do
+not find appropriate modifiers in the scroll down list, you can enter
+additional source information as text in the field at the bottom of the
+page. You may select as many modifiers as you want.
+
+#The following is a description of the available modifiers:
+
+#-Cell-line: Cell line from which sequence derives.
+
+#-Cell-type: Type of cell from which sequence derives.
+
+#-Chromosome: Chromosome to which the gene maps.
+
+#-Clone: Name of clone from which sequence was obtained.
+
+#-Clone-lib: Name of library from which sequence was obtained.
+
+#-Collected-by: Name of person who collected sample. Do not use
+accented or non-ASCII characters.
+
+#-Collection-date: Date sample was collected. Must use format
+23-Mar-2005, Mar-2005, or 2005.
+
+#-Country: The country of origin of DNA samples used for epidemiological
+or population studies.
+
+#-Dev-stage: Developmental stage of organism.
+
+#-Endogenous-virus-name: Name of inactive virus that is integrated into
+the chromosome of its host cell and can therefore exhibit vertical
+transmission.
+
+#-Environmental-sample: Identifies sequence derived by direct molecular
+isolation from an unidentified organism. Do not include extra text when
+using this modifier.
+
+#-Frequency: Frequency of occurrence of a feature.
+
+#-Fwd-PCR-primer-name: Name or designation of forward primer used for
+amplification.
+
+#-Fwd-PCR-primer-seq: Sequence of forward primer used for amplification.
+
+#-Genotype: Genotype of the organism.
+
+#-Germline: If the sequence shown is DNA and a member of the
+immunoglobulin family, this qualifier is used to denote that the sequence
+is from unrearranged DNA. Do not include extra text when using this
+modifier.
+
+#-Haplotype: Haplotype of the organism.
+
+#-Identified-by: Name of person who identified sample. Do not use
+accented or non-ASCII characters.
+
+#-Isolation-source: Describes the local geographical source of the organism
+from which the sequence was derived
+
+#-Lab-host: Laboratory host used to propagate the organism from which
+the sequence was derived.
+
+#-Lat-Lon: Latitude and longitude of location where sample was
+collected. Preferred format is decimal degrees N/S E/W.
+
+#-Map: Map location of the gene.
+
+#-Plasmid-name: Name of plasmid from which the sequence was obtained.
+
+#-Plastid-name: Name of plastid from which the sequence was obtained.
+
+#-Pop-variant: Name of the population variant from which the sequence was
+obtained.
+
+#-Rearranged: If the sequence shown is DNA and a member of the
+immunoglobulin family, this qualifier is used to denote that the sequence
+is from rearranged DNA. Do not include extra text when using this
+modifier.
+
+#Rev-PCR-primer-name: Name or description of reverse primer used for
+amplification.
+
+#Rev-PCR-primer-seq: Sequence of reverse primer used for amplification.
+
+#-Segment: Name of viral genome fragmented into two or more nucleic acid
+molecules.
+
+#-Sex: Sex of the organism from which the sequence derives.
+
+#-Subclone: Name of subclone from which sequence was obtained.
+
+#-Tissue-lib: Tissue library from which the sequence was obtained.
+
+#-Tissue-type: Type of tissue from which sequence derives.
+
+#-Transgenic: Identified organism that was the recipient of transgenic
+DNA. Do not include extra text when using this modifier.
+
+**Organism Subpage
+
+#Choose a modifier from the pull-down menu on the left side of the page
+and type the appropriate name on the right side of the page. If you do
+not find appropriate modifiers in the scroll down list, you can enter
+additional organism information as text in the field at the bottom of
+the page. You may select as many modifiers as you want.
+
+#The following is a description of the available modifiers:
+
+#-Acronym: Standard synonym (usually of a virus) based on the initials
+of the formal name. An example is HIV-1.
+
+#-Anamorph: The scientific name applied to the asexual phase of a fungus.
+
+#-Authority: The author or authors of the organism name from which sequence
+was obtained.
+
+#-Biotype: See biovar.
+
+#-Biovar: Variety of a species (usually a fungus, bacteria, or virus)
+characterized by some specific biological property (often geographical,
+ecological, or physiological). Same as biotype.
+
+#-Breed: The named breed from which sequence was obtained (usually applied
+to domesticated mammals).
+
+#-Chemovar: Variety of a species (usually a fungus, bacteria, or virus)
+characterized by its biochemical properties.
+
+#-Common: Common name of the organism from which sequence was obtained.
+
+#-Cultivar: Cultivated variety of plant from which sequence was obtained.
+
+#-Ecotype: The named ecotype (population adapted to a local habitat) from
+which sequence was obtained (customarily applied to populations of
+Arabidopsis thaliana).
+
+#-Forma: The forma (lowest taxonomic unit governed by the nomenclatural
+codes) of organism from which sequence was obtained. This term is usually
+applied to plants and fungi.
+
+#-Forma-specialis: The physiologically distinct form from which sequence
+was obtained (usually restricted to certain parasitic fungi).
+
+#-Group: Do not select this item.
+
+#-Isolate: Identification or description of the specific individual
+from which this sequence was obtained. An example is Patient X14.
+
+#-Old name: Do not select this item.
+
+#-Pathovar: Variety of a species (usually a fungus, bacteria or virus)
+characterized by the biological target of the pathogen. Examples
+include Pseudomonas syringae pathovar tomato and Pseudomonas syringae
+pathovar tabaci.
+
+#-Serogroup: See serotype.
+
+#-Serotype: Variety of a species (usually a fungus, bacteria, or virus)
+characterized by its antigenic properties. Same as serogroup and
+serovar.
+
+#-Serovar: See serotype.
+
+#-Specific-host: When the sequence submission is from an organism that
+exists in a symbiotic, parasititc, or other special relationship with
+some second organism, use this modifier to identify the name of the
+host species.
+
+#-Specimen-voucher: An identifier of the individual or collection of the
+source organism and the place where it is currently stored, usually an
+institution.
+
+#-Strain: Strain of organism from which sequence was obtained.
+
+#-Subgroup: Do not select this item.
+
+#-Sub-species: Subspecies of organism from which sequence was obtained.
+
+#-Substrain: Sub-strain of organism from which sequence was obtained.
+
+#-Subtype: Subtype of organism from which sequence was obtained.
+
+#-Synonym: The synonym (alternate scientific name) of the organism name
+from which sequence was obtained.
+
+#-Teleomorph: The scientific name applied to the sexual phase of a fungus.
+
+#-Type: Type of organism from which sequence was obtained.
+
+#-Variety: Variety of organism from which sequence was obtained.
+
+**GenBank Subpage
+
+#Please do not use this form. This field is reserved for information from
+NCBI's taxonomy database.
+
+*Miscellaneous Page
+
+**Synonyms Subpage
+
+#If there are alternative names for the organism from which the sequence
+was derived, enter them here. Please be aware that this is the
+appropriate field only for alternative names for the organism, not for
+alternative gene or protein names.
+
+**Cross-Refs Subpage
+
+#This page is for use by database staff only.
+
+>Publications
+
+*Overview: Descriptor or Feature?
+
+#Sequin allows two types of publications to be entered, Publication
+Descriptors and Publication Features. Publication Descriptors are
+bibliographic references that, like other descriptors, cover an entire
+sequence, or an entire set of sequences, in an entry. Publication
+Features are bibliographic references that, like other features, cover
+a specific interval on a given sequence.
+
+#Publications are entered into the Reference field of the database
+entry. References are citations of unpublished, in press, or published
+works that are relevant to the submitted sequence. Publications
+should provide information regarding the principle cloning and
+determination of the sequence within the record.
+
+#In general, there is one publication describing a sequence, and a
+Publication Descriptor should be used. To enter a Publication
+Descriptor, select Publications under the Annotate menu and click on
+Publication Descriptor.
+
+#However, if one publication describes the cloning of the 5' end of a
+gene, and another publication describes the cloning of the 3' end of
+the gene, Publication features may be used. To make a publication
+feature, choose Publication Feature in the Publications section of the
+Annotate menu. Enter the information about the publication, and then
+enter the nucleotide interval to which the publication refers on the
+Location page.
+
+*Citation on Entry Form
+
+**Status
+
+#Using the radio buttons, select one of the three options:
+
+#-Unpublished: Select this option if a manuscript has been written but
+not yet submitted or has been submitted for publication but has not yet
+been accepted.
+
+#-In Press: The article has been accepted for publication but is not yet
+in print.
+
+#-Published: The article has been published.
+
+**Class
+
+#Using the radio buttons, select the type of publication in which the
+sequence will appear.
+
+#-Journal
+
+#-Book Chapter
+
+#-Book
+
+#-Thesis/Monograph
+
+#-Proceedings Chapter: Abstract from a meeting
+
+#-Proceedings: A meeting
+
+#-Patent
+
+#-Online Publication: Used for journals which publish strictly online and
+do not issue print copies.
+
+#-Submission
+
+**Scope
+
+#Using the radio buttons, select one of the options.
+
+#-Refers to the entire sequence: Most publications should be classified
+as such.
+
+#-Refers to part of the sequence: For use only when a publication
+discusses only part of the presented sequence. You must enter the
+locations in the location tab in later forms. This selection is only
+valid when adding a Publication feature, not descriptor.
+
+#-Cites a feature on the sequence: This selection should only be made in
+limited cases. Its use must coincide with the use of the /citation
+qualifier on the given feature.
+
+#After you have filled out the Citation on Entry form, click on
+"Proceed" to see the next form.
+
+*Citation Information Form (General)
+
+**Authors Page
+
+***Names Subpage
+
+#Please enter the names of the authors. Note that the first name of the
+author is listed first. You can add as many authors to this page as
+necessary. After you type in the name of the third author, the box
+becomes a spreadsheet, and you can scroll down to the next line by
+using the thumb bar. The suffix toggle allows the addition of common
+suffixes to the author name. The consortium field should be used when
+a consortium is responsible for the sequencing or publication of the
+data. The consortium should not be the department or institute
+affiliation of the authors. Individual authors may be listed along
+with a consortium name.
+
+***Affiliation Subpage
+
+#Please enter information about the institution where the sequencing was
+performed.
+
+#Other pages in the Citation Information Form will be different,
+depending on the Class of publication selected in the Citation on Entry
+Form. Instructions for filling out the Citation Information Form for
+Journals is included here.
+
+*Citation Information Form (If Selected Class Was Journal)
+
+**Title Page
+
+#Enter title for manuscript in the box.
+
+**Journal Page
+
+#Fill in the appropriate Journal, Volume, Issue, Pages, Day, and Year
+fields by typing information into the boxes. Select the month with the
+pop-up menu. If necessary, choose an option from the Erratum pop-up
+menu and explain the erratum.
+
+#If you are running Sequin in its
+<A HREF="#NetConfigure">
+network-aware
+</A>
+mode, the program will look up the Title, Author, and Journal
+information in the MEDLINE database if you supply it with some minimal
+information. For example, if you know the MUID (MEDLINE Unique
+Identifier) of the publication, enter it in the appropriate box and
+select "Lookup By MUID." Sequin will automatically retrieve the rest
+of the information. One way to find the MUID of the publication is to
+look up the publication with the NCBI's
+
+<A HREF="http://www.ncbi.nlm.nih.gov/Entrez">
+Entrez
+</A>
+service. Alternatively, if you do not know the MUID, enter the Journal,
+Volume, Pages, and Year. Then select "Lookup Article". Sequin will
+retrieve the missing Title and Author information.
+
+#The PubStatus toggle is used by database staff. If you have used the
+"Lookup by MUID" or "Lookup by PMID" functions, this field may be
+populated. Please do not edit the information.
+
+**Remark Page
+
+#This page is reserved for use by the database staff.
+
+>File Menu
+
+*About Sequin
+
+#Details about the current version of Sequin.
+
+*Help
+
+#Launches the help documentation.
+
+*Open
+
+#Open an existing entry. This option will open a record that has been
+previously saved in Sequin. Furthermore, for analysis purposes, it can also
+open
+a FASTA-formatted sequence file. The sequence will be displayed in Sequin and
+can be analyzed with tools such as CDD Search, but it should not be submitted,
+because it does not have the appropriate annotations.
+
+*Close
+
+#Close this entry.
+
+*Export
+
+#Exports the currently displayed format to a file. Do not use export
+ASN1 for submission of sequences to the database.
+
+*Duplicate View
+
+#Duplicates the entry. You can then view the entry simultaneously in
+different Display Formats.
+
+*Save
+
+#Saves the entry. Note: This merely saves the entry so you can go back
+and edit it. It does not prepare the entry for submission to the
+database, that is, it does not validate the entry.
+
+*Save As
+
+#See Save.
+
+*Save as Binary Seq-entry
+
+#Saves the file in a compressed format and should be used only when the
+file is to be imported into other analysis programs. Do not use this
+option to save files for submission directly to GenBank.
+
+*Restore
+
+#Replaces the displayed record with a previously saved version. This
+feature is useful if you have made unwanted changes since you last saved
+the record.
+
+*Prepare Submission
+
+#Prepares the entry for submission to the database. See
+<A HREF="#SubmittingtheFinishedRecordtotheDatabase">
+Submitting the Finished Record to the Database
+</A>
+ in the Sequin help documentation.
+
+*Print
+
+#Prints the window that is currently selected. The selected window can
+be one of the Sequin forms or pages, or the help documentation.
+
+*Quit
+
+#Exit from Sequin.
+
+>Edit Menu
+
+*Copy
+
+#Copy the selected item.
+
+*Clear
+
+#Clear the selected item.
+
+*Edit Sequence
+
+#To edit a single sequence, select the sequence identifier in the Target
+Sequence pop-up menu, and click on Edit sequence. The sequence editor
+will be launched for that sequence. The
+<A HREF="#SequenceEditor">
+sequence editor
+</A>
+is discussed in more detail below.
+
+*Alignment Assistant
+
+#This option will launch the Alignment Assistant which is discussed in
+more detail
+
+<A HREF="#Workingwithsetsofalignedsequences">
+below
+</A>
+.
+
+*Edit Submitter Info
+
+#Opens up the Submission Instructions form, which allows you to enter
+additional information about the person submitting the record. Much of
+this information was entered on the first form in Sequin, the Submitting
+Authors form.
+
+#You can also save the information from the Submitting Authors form
+here, so that you can use it in subsequent Sequin submissions. Click
+on "Edit Submitter Info" and, under the file menu in the resulting
+Submission Instructions form, click on Export Submitter Info to save
+the information to a file. For subsequent Sequin submissions, if you
+have already saved the submittor information, click on Import Submitter
+Info under the File menu on the Submission page of the Submitting
+Authors form.
+
+**Submission Page
+
+#Indicate the type of submission. If it is a new submission, select
+New. If you are updating an existing submission in order to resubmit it
+to the databases, select Update. Check either the "Yes" or "No" radio
+button to indicate if the record should be released before publication.
+If you select "Yes", the entry will be released to the public after the
+database staff has added it to the database. If you select "No", fields
+will appear in which you can indicate the date on which the sequences
+should be released to the public. The submission will then be held back
+until formal publication of the sequence or
+GenBank Accession number, or until the Release Date, whichever comes
+first. If you have any special instructions, enter them in the box at
+the bottom of the page.
+
+**Contact Page
+
+#Update the name, affiliation, or contact numbers of the person
+submitting the record. Please supply a fax number to facilitate
+communication with database staff.
+
+**Citation Page
+
+#Update the names and affiliation of the people who should receive
+scientific credit for the generation of sequences in this entry. The
+address should list the principal institution in which the sequencing
+and/or analysis was carried out. If you are submitting the record as
+an update to the databases, explain the reason for the update on the
+Description subpage.
+
+*Update Sequence
+
+#This selection allows you to replace a sequence with another sequence,
+merge two sequences that overlap at their ends, 'patch' a corrected
+fragment of a sequence to the current sequence, or copy features from
+one sequence to another.
+
+#Use Single Sequence to import a sequence in FASTA or ASN.1 format (for
+example, a sequence record that has already been saved in Sequin). If
+you are running Sequin in
+
+<A HREF="#NetConfigure">
+Network Aware mode,
+</A>
+you can use Download Accession to import a record from Entrez. The
+Multiple Sequences option allows you to update multiple sequences using
+either FASTA or ASN.1 formats. In either format, each sequence
+identifier must be identical in the new and old sequences.
+
+#After you import the updated sequence, a new window will open that
+displays two graphical views and the text of the alignment of the new
+and old sequence. The first graphic displays the relative length of the
+two sequences and the length of the overlapping region between
+sequences. The second graphic represents any inserts, deletions, or
+point changes within the aligned region between the new and old
+sequences. Clicking on a region in this graphic will scroll to the
+corresponding nucleotide sequence in the alignment text below.
+
+#The Sequence Update box to the left shows the action that will be
+performed upon updating the sequence, i.e., no change, replace, extend
+5', extend 3', or patch. The patch function allows you to replace an
+internal fragment of the sequence without affecting flanking regions.
+You can also override the alignment between the new and old sequence
+using the Ignore alignment checkbox to force a sequence change of
+replace, Extend 5' or Extend 3'. This option allows you to append new
+sequence to with no overlap.
+
+#If the current sequence has annotation, you can use the Existing
+Features box to determine whether the annotation should remain or be
+removed upon updating the sequence. The Do not remove option is the
+default. However, you may chose to remove annotated features only in
+the aligned area, outside the aligned area, or to remove all currently
+annotated features.
+
+#When updating via Download Accession or an ASN.1 file, the Import
+Features box allows you to specify whether features from the new file
+should be imported to the existing record. The dialog offers
+different options for cases where the features on the new file are
+identical to those on the existing record.
+
+#If you are using the Multiple Sequences option, you may choose to
+review the sequences and update them one by one using the Update this
+Sequence box at the bottom of the window. You may skip a sequence
+update or choose to update all sequences at once without reviewing them
+in the Update Sequence dialog.
+
+#In any case, please carefully review the sequence and annotation in the
+record viewer after using the Update Sequence function.
+
+*Extend Sequence
+
+#This selection functions similar to the
+
+<A HREF="#UpdateSequence">
+Update Sequence
+</A>
+
+function. However, you can only extend the existing sequence in either
+the 5' or 3' direction in cases with no overlap between the existing
+and new sequences.
+
+*Feature Propagate
+
+#This selection allows you to propagate any annotated feature from one
+sequence in an aligned set to other sequences within the set. For
+example, if one nucleotide sequence in the alignment contains a CDS
+feature, you can annotate a similar CDS on the other nucleotide
+sequences in the set.
+
+#The default source of features to be propagated is the first member
+of the set. If you would like to use a different entry as the source of
+the features, scope to that entry in the Target Sequence menu before
+selecting Feature Propagate from the Edit menu.
+
+#The Feature Propagate window allows you to select which sequences
+should receive the new annotation and which features will be
+propagated. You can also select whether the features will be extended
+or split at gaps in the alignment. The split at gaps selection will
+produce two features, one on either side of the gap within the
+alignment. If you are propagating a CDS feature, you may specify that
+the translation end or extend through internal stop codons. You may
+also extend the translation after the stop codon on the source entry by
+chosing to translate the CDS after partial 3' boundary. If the CDS
+that you are propagating to other records is partial on either end, you
+should select the 'Cleanup CDS partials after propagation' check box.
+This will retain the partial nature of the CDS features on all records.
+ The fuse adjacent propagated intervals function will create one
+feature from two of the same type that contain abutting nucleotide
+intervals due to the nature of the alignment used for propagation.
+
+*Add Sequence
+
+#This selection allows you to add a new sequence to an existing
+population, mutation, phylogenetic, or environmental sample set.
+You may import the new entry in FASTA format or ASN.1 format (for
+example, a sequence record that has been saved in Sequin).
+
+*Parse File to Source
+
+#This selection allows you to add unique information for one source
+qualifier for each of the records in a batch or set. The input file
+must be in the format of a tab-delimited, two column table. The first
+column should list the SeqID exactly as it was listed in the original
+FASTA file. The second column should list the text value for the
+desired source qualifier for each record. Once the file has been
+imported, a pop-up box will appear with the source qualifiers listed in
+the pull down menus. The qualifiers are separated into three menus:
+one for taxonomic information, one for the Organism modifiers and one
+for the Source modifiers. For example, in order to add the clone
+designations 57 and 49 to the sequences labeled seq1 and seq2, the table
+
+seq1 57
+seq2 49
+
+should be used and clone should be selected from the Source modifiers
+pull-down menu.
+
+>Search Menu
+
+*Find ASN.1
+
+#Under this command, you can find and replace strings of letters in
+those fields of your submission that contain manually entered data.
+The fields that can be altered are Locus, Definition, Accession,
+Keywords, Source, Reference, and Features. To use this option, select
+Find and fill the Find and Replace lines with the appropriate text.
+Note that you cannot edit the sequence in this way.
+
+*Find FlatFile
+
+#Under this command, you can find strings of letters in all fields of
+your submission. You can use the Find First and Find Next buttons to
+identify the specified text sequentially through the flatfile.
+
+*Find by Gene
+
+#This option allows you to move quickly in the record viewer to a gene
+feature containing the specified gene symbol.
+
+*Find by Protein
+
+#This option allows you to move quickly in the record viewer to a CDS
+feature containing the specified product name.
+
+*Find by Position
+
+#This option allows you to move quickly in the record viewer to any
+feature annotated at the specified nucleotide location.
+
+*Validate
+
+#This option detects discrepancies between the format of your submission
+and that required by the database selected for entry. If discrepancies
+are present, it suggests ways in which to correct them. See the topic on
+
+<A HREF="#SubmittingtheFinishedRecordtotheDatabase">
+Submitting the Finished Record to the Database
+</A>
+ in the Sequin help documentation.
+
+*CDD Search
+
+#Performs a CDD BLAST search of the selected sequence against the
+NCBI's
+<A HREF="http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml">
+Conserved Domain Database
+</A>
+. To do a CDD BLAST search, Sequin must be in its network aware mode.
+
+#CDD currently contains domains derived from two popular collections,
+Smart and Pfam, plus contributions from colleagues at NCBI. The source
+databases also provide descriptions and links to citations. Since
+conserved domains correspond to compact structural units, CDs contain
+links to 3D-structure via Cn3D whenever possible.
+
+#The results of the CDD search will be displayed in the record
+viewer. These results are for your use only and should be removed
+from the record before submission.
+
+*Vector Screen
+
+#This option allows you to run a BLAST search of your nucleotide
+#sequence(s) against NCBI's
+<A HREF="http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html">
+UniVec
+</A>
+database. We highly recommend that you run this analysis and remove
+any vector contamination before submission. The UniVec database
+contains only one copy of every unique sequence segment from a large
+number of vectors. It also contains sequences for adapters, linkers
+and primers commonly used.
+
+#To run Vector screen on a submission containing multiple sequences,
+scope to ALL SEQUENCES in the Target Sequence pull-down before running
+the analysis. If there are many sequences, a status bar will appear
+indicating the progress of the search. If no contamination is found, a
+pop-up box will appear to notify you. If contamination is found, a
+miscellaneous feature will be annotated on the flatfile with the
+location of the contamination. Details will include the relative
+strength of the BLAST hit. You must trim the nucleotide sequence to
+remove this feature before submission.
+
+*ORF Finder
+
+#The ORF Finder shows a graphical representation of all the open reading
+frames (ORFs) in the nucleotide sequence. This tool allows you to
+select ORFs and have them appear as coding sequence (CDS) features on
+the sequence record.
+
+#The ORFs, indicated by colored boxes, are defined as the longest
+sequence containing a start codon and a stop codon. If the
+entire nucleotide sequence is an open reading frame but does not
+contain an initial start or a terminal stop codon, it will be indicated
+as an ORF as well. All six reading frames are shown; the top three
+boxes represent the plus strands, and the bottom three boxes the minus
+strands. The nucleotide sequence intervals of the ORFs are displayed in
+descending length order on the right side of the window. Intervals on
+the complementary (minus) strand are indicated by a 'c'. ORFs can be
+selected by clicking either directly on them or on the sequence
+interval. The ORF length button selects the length of ORFs that are
+displayed. For example, the default of 10 shows all ORFs that are
+greater than 10 nucleotides in length. Clicking on the box labelled ORF
+changes the display; potential start codons are indicated in white, and
+stop codons in red. ORFs can be selected in this display also. The
+definition of start and stop codons is dependent on the genetic code
+that was selected. Be sure to choose the appropriate genetic code for
+translating the sequence before opening the ORF finder.
+
+*Select Target
+
+#This option changes the sequence that is selected in the Target
+Sequence pop-up. Type the SeqID of the sequence in the box, and the
+record viewer will be updated to display that sequence.
+
+>Misc Menu
+
+*Style Manager
+
+#The Style manager allows you to choose between different formats in
+which to view the Graphical Display Format. The graphical display is
+selected by choosing the Graphic display format on the record viewer.
+Using the Style Manager, you can also copy the style or modify it to
+suit your needs.
+
+*Net Configure
+
+#As a default, Sequin is available as a stand-alone program. However,
+the program can also be configured to exchange information with the NCBI
+(GenBank) over the Internet. The network-aware mode of Sequin is
+identical to the stand-alone mode, but it contains some additional
+useful options.
+
+#Sequin will only function in its network-aware mode if the computer on
+which it resides has a direct Internet connection. Electronic mail
+access to the Internet is insufficient. In general, if you can install
+and use a WWW browser on your system, you should be able to install and
+use network-aware Sequin. Check with your system administrator or
+Internet provider if you are uncertain as to whether you have direct
+Internet connectivity.
+
+#There are two ways to change Sequin into its network-aware mode. If
+you are still on the initial Welcome to Sequin form, select Net
+Configure under the Misc menu. If you have already worked on a Sequin
+submission and are looking at the record in the record viewer, select
+the Net Configure option from the Misc menu.
+
+#Most users will be able to use the default (Normal) settings on the
+Network Configuration page; select Accept to complete the configuration
+process.
+
+#If a "Normal" Connection does not work, you may need to select the
+Firewall Connection. Contact your system administrator to determine
+what to enter into the Proxy and Port fields. If you do not have
+access to the domain name server (DNS), uncheck this box.
+
+#The Timeout pop-up selects the length of time that your local copy of
+Sequin will wait for a reply from the NCBI server. You may need to set
+this number higher (i.e., 60 seconds or 5 minutes) if you are outside
+of the United States or have a bad internet connection.
+
+#If you have problems setting up the network configuration, contact
+
+<a href="mailto:info@ncbi.nlm.nih.gov">
+info@ncbi.nlm.nih.gov.
+</a>
+
+#If you would like to change Sequin back to its stand-alone mode, select
+Net Configure again from the Misc menu. Click on Connection: None.
+
+#The network-aware mode of Sequin allows you to perform a number of
+additional, important functions. These functions all appear as
+additional menu items. A brief description of these functions follows.
+Further descriptions are available as indicated elsewhere in the help
+documentation.
+
+**Updating Existing GenBank Records
+
+#Using Sequin in its network-aware mode, you can download an existing
+GenBank record from Entrez using the GenBank accession number or GI
+identification number (NID). You can then use Sequin to make any
+necessary changes to the record, and resubmit it to GenBank as a
+sequence update.
+
+<A HREF="#WelcometoSequinForm">
+Instructions
+</A>
+for submitting sequence updates are presented under the Welcome to
+Sequin Form. You can download any record from Entrez and look at it in
+Sequin. However, you can only formally update those records which you
+have submitted since submitters retain editorial control of their
+records.
+
+**Performing a PubMed Look-Up
+
+#In its network-aware mode, Sequin can import the relevant sections of a
+PubMed record directly into a sequence submission record. Rather than
+typing in the entire citation, you can enter minimal information, such
+as the PubMed Unique Identifier (PMID), or Journal name, volume, year,
+and pages. The
+
+<A HREF="#JournalPage">
+PubMed lookup
+</A>
+is explained in the section of the documentation entitled Publications.
+
+**Performing a Taxonomy Look-up
+#In its network-aware mode, Sequin can look
+up the taxonomic lineage of an organism from the NCBI's Taxonomy
+database. This look-up is normally performed by the NCBI database staff
+after the record has been submitted to GenBank. If you look up the
+taxonomy before submitting the sequence, you can make a note in the
+record of any disagreements. The
+<A HREF="#LineageSubpage">
+taxonomy lookup
+</A>
+is explained in the section of the documentation covering
+Biological Source: Organism page: Lineage subpage.
+
+**Accessing the NCBI DeskTop
+#The NCBI DeskTop displays the internal
+structure of the record being viewed in Sequin. The
+<A HREF="#NCBIDeskTop">
+DeskTop
+</A>
+is explained under the Misc menu.
+
+*NCBI DeskTop
+
+#This option is only available if you are running Sequin in its
+<A HREF="#NetConfigure">
+network-aware
+</A>
+mode.
+
+#The NCBI DeskTop provides a view of the internal structure of the
+Sequin record, the ASN.1. Its display resembles a Venn diagram and
+represents all the structures represented in the ASN.1 data model.
+
+#In addition, a number of undocumented software tools from the NCBI can
+be accessed from the DeskTop. These tools are components of the NCBI
+portable software Toolkit. You can also customize these functions using
+the Toolkit with your own software tools. The Toolkit and its
+documentation are available from the NCBI by anonymous
+<A HREF="ftp://ftp.ncbi.nih.gov/toolbox/README">
+FTP.
+</A>
+
+#The DeskTop should only be used by very seasoned users. At this time,
+we are not providing any documentation for these specialized functions.
+
+>Annotate Menu
+
+#This menu allows you to enter features and descriptors on the sequence.
+
+#The first six options, Genes and Named Regions, Coding Regions and
+Transcripts, Structural RNAs, Bibliographic and Comments, Sites and
+Bonds, and Remaining Features refer to types of Features that can be
+added to the sequence. Features are described in more detail in the
+above section entitled
+<A HREF="#Features">
+Features.
+</A>
+
+#If you are submitting a set of similar sequences, you can add the same
+feature across the entire span of each by using the Batch Feature Apply
+option. The feature must span the entire nucleotide sequence of each
+member; you can not annotate specific nucleotide locations using this
+option (for this, see
+
+<A HREF="#FeaturePropagate">Feature Propagate</A>).
+
+For each feature, you will be prompted to designate whether the feature
+is 5' or 3' partial and whether is is on the plus or minus strand. You
+may also add a comment or other qualifier to the feature. The Add
+Qualifier option allows you to add a qualifier to an existing feature.
+You must specify the feature and qualifier in the Add Qualifier pop-up
+box. Source qualifiers can be added to all entries using the Add
+Source Qualifier option. Qualifiers specific to the CDS and gene can
+be added using Add CDS-Gene-Prot-mRNA and RNA qualifiers using Add RNA
+Qual. In each case, a pop-up box appears with qualifier options
+appropriate for that feature.
+
+#The Batch Feature Edit function allows you to edit existing qualifiers.
+ For each menu choice, a pop-up box allows you to select the feature
+containing the qualifier and the specific qualifier to be edited. You
+can use the Find/Replace text boxes to edit the information contained
+within the qualifier.
+
+#The Publications option allows you to add a Publication Feature or
+Publication Descriptor to the record. Publications are described in
+more detail in the above section entitled
+
+<A HREF="#Publications">
+Publications.
+</A>
+
+#The Descriptors option allows you to add Descriptors to the
+record. Descriptors are described in more detail in the section
+entitled
+<A HREF="#Descriptors">
+Descriptors,
+</A>
+above.
+
+#The Generate Definition Line option will generate a title for your
+sequence based on the information provided in the record. This option
+will work for single sequences as well as sets of sequences, and can
+handle complex annotations with multiple features. The title will
+follow GenBank conventions, but may be modified by the database staff
+if it is not appropriate. The title you enter here will replace any
+title you entered elsewhere in the submission, for example, any title
+that was attached to the nucleotide sequence. For a description of
+definition lines, see
+
+<A HREF="#NucleotideDefinitionLine(Title)">
+Nucleotide Definition Line (Title)
+</A>
+, above.
+
+>Options Menu
+
+*Font
+
+#Use this item to change the display font. From the pop-up menus,
+choose the style and size of type. For additional changes, mark the
+Bold, Italic, or Underline check boxes. The default font is 10-point
+Courier.
+
+>Sequence Editor
+
+#This editor allows you to modify the nucleotide or amino acid sequences
+and corresponding annotation in your entry. Although the Sequence Editor
+does allow you to undo changes you make to the sequence, we strongly
+suggest that you save a copy of the entry before launching the Sequence
+Editor so that you can revert to it if necessary.
+
+*Starting the Sequence Editor
+
+#The sequence that appears in the editor is dependent on the sequence(s)
+selected in the Target Sequence pull-down list. There are two ways to
+launch the sequence editor for nucleotide sequences. First, you can
+double click within sequence in any display format of the record viewer.
+A window containing the DNA sequence will appear. Second, in the record
+viewer, select the sequence that you would like to edit in the Target
+Sequence pop-up menu. Click on Edit Sequence under the Edit menu. You
+can launch the editor for protein sequences by selecting the protein
+sequence in the Target Sequence pop-up menu and double clicking within
+the protein sequence. A window containing the protein sequence will
+appear.
+
+*Moving around the Sequence Editor
+
+#The cursor can be moved with the mouse or the arrow keys. The display
+window will change to show the position of the cursor. The sequence
+location of the first residue on each line is indicated on the left side
+of the window. The cursor location, or the range of sequences selected
+by the mouse, is shown in the upper left corner of the window. If you
+want to move the cursor to a specific location, type the number in the
+box on the top left of the sequence editor window, and hit the Go to
+button. If you want to look at a specific sequence, but not move the
+cursor to it, type the number in the upper right box of the window and
+hit the Look at button.
+
+*Editing Sequence and Existing Annotation
+
+#Select a piece of sequence by highlighting it with the mouse. To
+select the entire sequence, click on a sequence location number on the
+left side of the window. Any sequence that is highlighted in the
+Sequence Editor will show up as a box on the sequence when it is viewed
+in the Graphic Display Format.
+
+#One way to insert and delete residues is with the mouse. Move the
+cursor to the appropriate location and type. Text will be inserted to
+the left of the cursor. Delete sequence with the backspace or delete
+key. Text will be deleted to the left of the cursor. To delete a block
+of sequence, highlight it with the mouse and use the delete or backspace
+key.
+
+#Another way to insert and delete residues is with options under the Edit
+menu of the Sequence Editor. Use Cut to remove, or Copy to copy,
+highlighted residues. Copied residues can then be pasted elsewhere
+within the sequence by using the Paste option.
+
+#Features annotated via the record viewer will be displayed in a
+graphical format within the sequence editor. CDS features will be be
+displayed as a blue line across the appropriate nucleotide location. All
+other features will be displayed as a black line. To the left of the
+line, the name of the feature is displayed. In the case of CDS or mRNA
+features, the product name is shown. For gene features, the gene locus
+is shown.
+
+#Double-clicking on the feature will launch the feature editor just as in
+the record viewer. However, you can also change the nucleotide location
+of any feature within the graphical view. To move the entire feature,
+select the feature and drag it to the appropriate location while holding
+down the mouse button. To alter the 5' or 3' end of a feature, click on
+the feature's end and drag to the new location while holding down the
+mouse button.
+
+#Before moving the nucleotide locations of a CDS feature, it may be
+useful to view the codons in the current translation. You can do this by
+clicking on the feature line and releasing the mouse button. A grid will
+be displayed that shows the triplet location for the current annotation.
+Once you have changed the nucleotide location of a CDS feature in the
+graphical view, you can see the new translation by using the Translate
+CDS button at the bottom of the window.
+
+#To save changes you have made to the sequence, press the Accept button
+at the bottom of the Sequence Editor display window. If you do not want
+to save the changes, press the Cancel button at the bottom of the
+Sequence Editor display window. Selecting either Accept or Cancel will
+quit the Sequence Editor and return you to the record viewer. Any
+changes you make will not become a permanent part of the Sequin record
+until you Save the record in the record viewer.
+
+#New features can be added using the Features menu.
+
+*Sequence Editor Window Buttons
+
+**Go to
+
+#Moves the cursor to the indicated location.
+
+**Look at
+
+#Moves the window to the indicated location without moving the cursor.
+
+**Merge Feature Mode/Split Feature Mode
+
+#In merge mode, any new sequence that is entered into a region spanned
+by an existing feature becomes part of that feature. For example, if
+you enter new sequence in the middle of a CDS, that sequence will be
+translated as part of the CDS. In split mode, the new sequence
+interrupts the feature. For example, if you enter new sequence in the
+middle of a CDS, the CDS will be interrupted by that sequence (see the
+location of the CDS in the record viewer).
+
+**Numbering
+
+#Allows the sequence location numbering to be hidden, displayed on the
+side, or displayed on the top of the sequence.
+
+**Grid
+
+#Allows the display to show a grid separating each feature and sequence
+for easier viewing.
+
+**Show/Hide Features
+
+#This box toggles between hiding and showing the features on a sequence.
+
+**Accept
+
+#Closes the Sequence Editor after saving all of the changes made to
+sequences and features.
+
+**Cancel
+
+#Closes the Sequence Editor without saving any changes made to sequences or
+features.
+
+**Translate CDS
+
+#Allows translation of coding region features after the location has been
+changed within the graphical view.
+
+*Sequence Editor File Menu
+
+**Export
+
+#Allows the export of a range of sequence as a FASTA file or text file.
+Using the text option will also export overlapping features if they are
+displayed. If the features are first hidden, only the sequence will be
+exported. All protein translations displayed at the time of export, will
+be exported as well.
+
+**Accept
+
+#Closes the Sequence Editor after saving all of the changes made to
+sequence and features.
+
+**Cancel
+
+#Closes the Sequence Editor without saving any changes made to sequences
+of features.
+
+*Sequence Editor Edit Menu
+
+**Undo
+
+#Undoes all actions performed in the Sequence Editor since the last save.
+
+**Redo
+
+#Restores changes removed with Undo option
+
+**Cut
+
+#Removes the highlighted sequence. This sequence can be pasted elsewhere.
+
+**Paste
+
+#Pastes a cut or copied sequence to the right of the cursor.
+
+**Copy
+
+#Copies the highlighted sequence. This sequence can be pasted elsewhere.
+
+**Find
+
+#Allows you to find DNA or amino acid sequence patterns in your sequence.
+ The search is case insensitive. To find an exact match to a DNA
+sequence pattern, type the pattern in the box. The number of items found
+will be displayed and you can toggle through each instance with the Find
+Next button. To find the reverse complement of the pattern, click on
+the reverse complement box at the bottom of the pop-up box.
+
+#To find an exact match to an amino acid seqeunce pattern, type that
+sequence in the box, and click on "translate sequence". Sequin will look
+for all occurrences of that pattern in all six open reading frames. The
+DNA sequence encoding that protein sequence in any of the six reading
+frames will be hightlighted.
+
+**Translate CDS
+
+#Allows translation of coding region features after the location has been
+changed within the graphical view.
+
+**Complement
+
+#Shows the complement of the submitted strand underneath the original.
+
+**Reading Frames
+
+#Shows the indicated phase translation of the selected coding sequence.
+You can select any or all of the six reading frames, all reading frames
+or all positive or negative frames.
+
+**Protein Mismatches
+
+#Indicates amino acid which does not match conceptual translation
+following a nucleotide sequence change. The original amino acid sequence
+will be displayed until the Translate CDS function is used. Differences
+will be indicated by a red box around the amino acid abbreviation.
+
+**On-the-fly Protein Translations
+
+#Creates a second amino acid sequence in the display which retranslates
+as the nucleotide sequence is changed to allow side-by-side comparison to
+the original amino acid sequence.
+
+*Sequence Editor Features Menu
+
+#The menu contains a long list of all features that can be annotated on a
+sequence. These features are the same as those that are accessible
+through the main Sequin Annotate menu.
+
+#You can annotate features either in the Annotate menu or in the Sequence
+Editor. If you annotate them in the Annotate menu, you must type in the
+nucleotide sequence location of the feature. However, if you add
+features from the Sequence Editor, you can highlight the sequence that
+the feature covers, and the location of the sequence will be
+automatically entered in the feature location box. Additional
+explanations of how to annotate features are provided in the section on
+<A HREF="#Features">
+Features.
+</A>
+
+>Working with Sets of Aligned Sequences
+
+#Sequin allows you to work with aligned sets of closely related
+nucleotide sequences that are part of a population, phylogenetic, or
+mutation study. If the sequences are imported in a pre-aligned format,
+such as PHYLIP, Sequin uses this alignment. If the sequences are
+imported individually in FASTA format, Sequin can generate its own
+alignment.
+
+#You can view the aligned sequences in the Sequence Alignment Editor. In
+the record viewer, select All Sequences in the Target Sequences menu,
+and select the Alignment Display Format.
+
+#The Alignment Assistant is launched by selecting Alignment Assistant
+from the Edit menu in the record viewer. It can be used to apply
+features to the whole set of sequences using the alignment coordinates.
+Rather than calculating the nucleotide coordinates for every feature on
+every nucleotide sequence, you may select the feature's location using
+its alignment coordinates and apply it to every member of the set
+simultaneously. Sequin will calculate the nucleotide locations as they
+apply to each member of the set.
+
+*Alignment Assistant Window Buttons
+
+**Go to
+
+#The Go to alignment position and Go to sequence position buttons both
+scroll the aligment assistant so that the requested position is
+visible. If the requested position is already visible, nothing will
+happen. Unlike the Sequence editor window, the 'go to' button does not
+control the cursor position.
+
+**Numbering
+
+#Allows the sequence location numbering to be hidden, displayed on the
+side, or displayed on the top of the sequence.
+
+**Grid
+
+#Allows the display to show a grid separating each feature and sequence for easier viewing.
+
+**Features Toggle
+
+#It is possible to view annotated features in the aligment assistant.
+The features are displayed as a bar underneath the coordinates for that
+feature. The identity of the feature is displayed in the left-hand
+column. The default selection is to have the features Hidden. You may
+display the features associated only with the Target Sequence or
+features annotated on All Sequences in the alignment.
+
+*Alignment Assistant File Menu
+
+**Export
+
+#Allows you to export the alignment to a file in three different
+formats. The contiguous and interleaved options export the alignment
+accordingly in FASTA+GAP format. The text representation option saves
+the alignment as it appears in the Alignment Assistant. Note that with
+this option features are included if they are displayed at the time of
+export.
+
+**Close
+
+#Closes the Alignment Assistant window and saves any changes made.
+
+*Alignment Assistant Edit Menu
+
+**Remove Sequences from Alignment
+
+#Allows you to remove selected sequence(s) from the alignment. Select
+the sequence by clicking on it. You can select multiple sequences by
+holding down the control key. The sequence will then be highlighted in
+grey. Note that this option will remove the sequence from the
+alignment, but it is still present in your submission.
+
+**Validate Alignment
+
+#Checks for problems with the alignment. If errors are reported, please
+review and attempt to fix your alignment before submission.
+
+**Propagate Features
+
+#This function is the same as that available under the Edit Menu in the
+record viewer. A full description is available
+
+<A HREF="#FeaturePropagate">
+above
+</A>
+.
+
+*Alignment Assistant View Menu
+
+**Target
+
+#Allows you to select a sequence within the alignment as the target
+sequence. This can also be done by double-clicking on the sequence
+within the alignment. The SeqID of the target sequence will be
+displayed in red. Features can be displayed on the target sequence
+only and it is the sequence used for comparison in the
+
+<A HREF="#ShowSubstitutions">
+Show Substitutions
+</A>
+view.
+
+**Show Substitutions
+
+#Changes the alignment view so that identities are replaced with a "."
+and only substitutions are shown. The substitutions and identities are
+relative to the selected target sequence.
+
+*Alignment Assistant Features Menu
+
+#Allows the annotation of features to a single sequence or all sequences
+within the alignment. All features available in this menu are
+discussed through the main Sequin Annotate menu.
+
+#Select the feature location by clicking the start location on one of
+the sequences, keeping the mouse button depressed, drag the cursor to
+the end of the feature location. The selected area will now be
+underlined and red and the alignment coordinates of this area will be
+displayed in the upper left of the Alignment Assistant window.
+
+**Apply to Target Sequence
+
+#Allows you to choose a feature to be applied only to the target
+sequence. The locations may be entered manually or can be determined
+based on highlighting the sequence as described above.
+
+**Apply to Alignnent
+
+#Allows you to add the selected feature to all sequences within your
+alignment based on the alignment coordinates you have selected. Note
+that in the feature pop-up boxes in this menu, the Location will always
+be entered as the location relative to the alignment coordinates.
+
+<HR>
+
+<CENTER>
+<P> 
+<P CLASS=medium1><B>Questions or Comments?</B>
+<BR>Write to the <A HREF="mailto:info@ncbi.nlm.nih.gov">NCBI Service
+Desk</A></P>
+<P CLASS=medium1>Revised December 2, 2005
+
+</CENTER>
+
+<!-- end of content -->
+
+</body>
+</html>
+
--- /dev/null
+52
+gt >
+lt <
+amp &
+agr alpha
+Agr Alpha
+bgr beta
+Bgr Beta
+ggr gamma
+Ggr Gamma
+dgr delta
+Dgr Delta
+egr epsilon
+Egr Epsilon
+zgr zeta
+Zgr Zeta
+eegr eta
+EEgr Eta
+thgr theta
+THgr Theta
+igr iota
+Igr Iota
+kgr kappa
+Kgr Kappa
+lgr lambda
+Lgr Lambda
+mgr mu
+Mgr Mu
+ngr nu
+Ngr Nu
+xgr xi
+Xgr Xi
+ogr omicron
+Ogr Omicron
+pgr pi
+Pgr Pi
+rgr rho
+Rgr Rho
+sgr sigma
+Sgr Sigma
+sfgr s
+tgr tau
+Tgr Tau
+ugr upsilon
+Ugr Upsilon
+phgr phi
+PHgr Phi
+khgr chi
+KHgr Chi
+psgr psi
+PSgr Psi
+ohgr omega
+OHgr Omega
+
+
--- /dev/null
+13
+Acanthamoeba healyi 1 4 INV 65661
+Acanthocybium solandri 1 2 VRT 13323
+Acanthopanax sessiliflorus 1 1 PLN 105886
+Acetabularia acetabulum 6 1 PLN 35845
+Acidithiobacillus ferrooxidans 11 0 BCT 920
+Acipenser baerii Siberian sturgeon 1 2 VRT 27689
+Acrossocheilus paradoxus 1 2 VRT 76593
+Actinobacillus actinomycetemcomitans 11 0 BCT 714
+Actinobacillus pleuropneumoniae 11 0 BCT 715
+Acyrthosiphon pisum pea aphid 1 5 INV 7029
+Aedes aegypti yellow fever mosquito 1 5 INV 7159
+Aegilops speltoides 1 1 PLN 4573
+Aegilops tauschii 1 1 PLN 37682
+Aepyceros melampus impala 1 2 MAM 9897
+Aequorea victoria 1 4 INV 6100
+Aeromonas hydrophila 11 0 BCT 644
+African swine fever virus 1 0 VRL 10497
+Agaricus bisporus 1 4 PLN 5341
+Agrobacterium tumefaciens 11 0 BCT 358
+Aids-associated retrovirus 1 0 VRL 11966
+Ajellomyces capsulatus 1 4 PLN 5037
+Alexandrium tamarense 1 4 PLN 2926
+Allium cepa onion 1 1 PLN 4679
+Allium sativum garlic 1 1 PLN 4682
+Alstroemeria peruviana 1 1 PLN 245552
+Amblyomma americanum 1 5 INV 6943
+Amblyomma variegatum 1 5 INV 34610
+Amborella trichopoda 1 1 PLN 13333
+Ambystoma maculatum spotted salamander 1 2 VRT 43114
+Ambystoma mexicanum axolotl 1 2 VRT 8296
+Amphidinium carterae 1 4 PLN 2961
+Anaplasma marginale 11 0 BCT 770
+Anaplasma phagocytophilum 11 0 BCT 948
+Anas fulvigula 1 2 VRT 75846
+Anas platyrhynchos 1 2 VRT 8839
+Ancylostoma caninum dog hookworm 1 5 INV 29170
+Ancylostoma ceylanicum 1 5 INV 53326
+Anguilla japonica Japanese eel 1 2 VRT 7937
+Anolis sagrei brown anole 1 2 VRT 38937
+Anopheles arabiensis 1 5 INV 7173
+Anopheles funestus 1 5 INV 62324
+Anopheles gambiae African malaria mosquito 1 5 INV 7165
+Anopheles maculipennis 1 5 INV 41429
+Antheraea yamamai Japanese oak silkmoth 1 5 INV 7121
+Antirrhinum majus snapdragon 1 1 PLN 4151
+Aotus nancymaae Ma's night monkey 1 2 PRI 37293
+Apis mellifera honey bee 1 5 INV 7460
+Apium graveolens 1 1 PLN 4045
+Aplysia californica California sea hare 1 5 INV 6500
+Apodemus sylvaticus European woodmouse 1 2 ROD 10129
+Arabidopsis lyrata 1 1 PLN 59689
+Arabidopsis suecica 1 1 PLN 45249
+Arabidopsis thaliana thale cress 1 1 PLN 3702
+Arachis hypogaea peanut 1 1 PLN 3818
+Araneus ventricosus 1 5 INV 182803
+Archaeoglobus fulgidus 11 0 BCT 2234
+Argopecten irradians 1 5 INV 31199
+Artemia franciscana 1 5 INV 6661
+Ascaris lumbricoides common roundworm 1 5 INV 6252
+Ascaris suum pig roundworm 1 5 INV 6253
+Ashbya gossypii 1 3 PLN 33169
+Asparagus officinalis garden asparagus 1 1 PLN 4686
+Aspergillus flavus 1 4 PLN 5059
+Aspergillus fumigatus 1 4 PLN 5085
+Aspergillus nidulans 1 4 PLN 162425
+Aspergillus niger 1 4 PLN 5061
+Aspergillus oryzae 1 4 PLN 5062
+Aspergillus terreus 1 4 PLN 33178
+Aspergillus tubingensis 1 4 PLN 5068
+Ateles geoffroyi black-handed spider monkey 1 2 PRI 9509
+Avena sativa oat 1 1 PLN 4498
+Avian infectious bronchitis virus 1 0 VRL 11120
+Avicennia marina 1 1 PLN 82927
+Azotobacter vinelandii 11 0 BCT 354
+B19 virus 1 0 VRL 10798
+Bacillus anthracis 11 0 BCT 1392
+Bacillus atticus 1 5 INV 36825
+Bacillus cereus 11 0 BCT 1396
+Bacillus clausii 11 0 BCT 79880
+Bacillus grandii 1 5 INV 55088
+Bacillus licheniformis 11 0 BCT 1402
+Bacillus lynceorum 1 5 INV 73234
+Bacillus subtilis 11 0 BCT 1423
+Bacillus thuringiensis 11 0 BCT 1428
+Bacillus whitei 1 5 INV 57870
+Bacteroides fragilis 11 0 BCT 817
+Beauveria bassiana 1 4 PLN 176275
+Bemisia tabaci 1 5 INV 7038
+Beta vulgaris 1 1 PLN 161934
+Betula pendula European white birch 1 1 PLN 3505
+Bifidobacterium longum 11 0 BCT 216816
+Biomphalaria glabrata bloodfluke planorb 1 5 INV 6526
+Biomphalaria pfeifferi 1 5 INV 112525
+Biphyllus lunatus 1 5 INV 197003
+Bluetongue virus 1 0 VRL 40051
+Blumeria graminis 1 4 PLN 34373
+Bombyx mandarina wild silkworm 1 5 INV 7092
+Bombyx mori domestic silkworm 1 5 INV 7091
+Boophilus microplus southern cattle tick 1 5 INV 6941
+Bordetella bronchiseptica 11 0 BCT 518
+Bordetella pertussis 11 0 BCT 520
+Borrelia afzelii 11 0 BCT 29518
+Borrelia burgdorferi Lyme disease spirochete 11 0 BCT 139
+Borrelia garinii 11 0 BCT 29519
+Bos indicus zebu 1 2 MAM 9915
+Bos taurus cow 1 2 MAM 9913
+Bothrops insularis island jararaca 1 2 VRT 8723
+Botryllus schlosseri 1 13 INV 30301
+Botryotinia fuckeliana 1 4 PLN 40559
+Bovine respiratory syncytial virus 1 0 VRL 11246
+Bradyrhizobium japonicum 11 0 BCT 375
+Branchiostoma belcheri 1 5 INV 7741
+Branchiostoma floridae Florida lancelet 1 5 INV 7739
+Brassica campestris 1 1 PLN 3711
+Brassica juncea 1 1 PLN 3707
+Brassica napus rape 1 1 PLN 3708
+Brassica oleracea 1 1 PLN 3712
+Brassica rapa 1 1 PLN 3711
+Brucella melitensis 11 0 BCT 29459
+Brugia malayi 1 5 INV 6279
+Bruguiera gymnorrhiza 1 1 PLN 39984
+Bubalus bubalis water buffalo 1 2 MAM 89462
+Buchnera aphidicola 11 0 BCT 9
+Burkholderia cepacia 11 0 BCT 292
+Burkholderia fungorum 11 0 BCT 134537
+Burkholderia pseudomallei 11 0 BCT 28450
+Caenorhabditis briggsae 1 5 INV 6238
+Caenorhabditis elegans 1 5 INV 6239
+Callithrix jacchus white-tufted-ear marmoset 1 2 PRI 9483
+Callosobruchus maculatus cowpea weevil 1 5 INV 64391
+Camelus dromedarius Arabian camel 1 2 MAM 9838
+Campylobacter jejuni 11 0 BCT 197
+Candida albicans 12 4 PLN 5476
+Candida famata 1 3 PLN 4959
+Candida glabrata 1 3 PLN 5478
+Candida tropicalis 12 3 PLN 5482
+Candidula unifasciata 1 5 INV 100452
+Canis familiaris dog 1 2 MAM 9615
+Capra hircus goat 1 2 MAM 9925
+Caprine arthritis-encephalitis virus 1 0 VRL 11660
+Capsicum annuum 1 1 PLN 4072
+Capsicum chinense 1 1 PLN 80379
+Carabus granulatus 1 5 INV 118799
+Carassius auratus goldfish 1 2 VRT 7957
+Carica papaya papaya 1 1 PLN 3649
+Caulobacter crescentus 11 0 BCT 155892
+Caulobacter vibrioides 11 0 BCT 155892
+Cavia porcellus domestic guinea pig 1 2 ROD 10141
+Ceratitis capitata Mediterranean fruit fly 1 5 INV 7213
+Ceratodon purpureus 1 1 PLN 3225
+Ceratopteris richardii 1 1 PLN 49495
+Cercopithecus aethiops African green monkey 1 2 PRI 9534
+Cervus elaphus red deer 1 2 MAM 9860
+Chaetodipus intermedius rock pocket mouse 1 2 ROD 38666
+Chaetomium globosum 1 4 PLN 38033
+Chlamydia trachomatis 11 0 BCT 813
+Chlamydomonas reinhardtii 1 1 PLN 3055
+Chlamydophila pneumoniae 11 0 BCT 83558
+Chlamydotis undulata 1 2 VRT 172680
+Chlorobium tepidum 11 0 BCT 1097
+Chloroflexus aurantiacus 11 0 BCT 1108
+Cicer arietinum chickpea 1 1 PLN 3827
+Cicindela campestris 1 5 INV 150234
+Ciona intestinalis 1 13 INV 7719
+Ciona savignyi 1 13 INV 51511
+Citrullus lanatus watermelon 1 1 PLN 3654
+Citrus reticulata 1 1 PLN 85571
+Citrus sinensis 1 1 PLN 2711
+Citrus tristeza virus 1 0 VRL 12162
+Citrus unshiu 1 1 PLN 55188
+Citrus x paradisi 1 1 PLN 37656
+Cladosporium fulvum 1 4 PLN 5499
+Cleome hassleriana 1 1 PLN 28532
+Clonorchis sinensis 1 9 INV 79923
+Clostridium acetobutylicum 11 0 BCT 1488
+Clostridium difficile 11 0 BCT 1496
+Clostridium perfringens 11 0 BCT 1502
+Clostridium thermocellum 11 0 BCT 1515
+Coccidioides immitis 1 4 PLN 5501
+Codonopsis lanceolata 1 1 PLN 103999
+Coffea arabica coffee 1 1 PLN 13443
+Colletotrichum gloeosporioides 1 4 PLN 5457
+Colletotrichum trifolii 1 4 PLN 5466
+Columba livia domestic pigeon 1 2 VRT 8932
+Conidiobolus coronatus 1 4 PLN 34488
+Cooperia oncophora 1 5 INV 27828
+Coprinopsis cinerea 1 4 PLN 5346
+Coprinus cinereus 1 4 PLN 5346
+Cordyceps bassiana 1 4 PLN 176275
+Coregonus clupeaformis 1 2 VRT 59861
+Corynebacterium glutamicum 11 0 BCT 1718
+Corynebacterium pseudotuberculosis 11 0 BCT 1719
+Coturnix coturnix common quail 1 2 VRT 9091
+Coturnix japonica Japanese quail 1 2 VRT 93934
+Crassostrea gigas Pacific oyster 1 5 INV 29159
+Crassostrea virginica eastern oyster 1 5 INV 6565
+Cricetulus griseus Chinese hamster 1 2 ROD 10029
+Crocus sativus 1 1 PLN 82528
+Cryphonectria parasitica 1 4 PLN 5116
+Cryptococcus bacillisporus 1 4 PLN 37769
+Cryptococcus neoformans 1 4 PLN 5207
+Cryptomeria japonica Japanese cedar 1 1 PLN 3369
+Cryptosporidium parvum 1 4 INV 5807
+Ctenocephalides felis cat flea 1 5 INV 7515
+Ctenopharyngodon idella grass carp 1 2 VRT 7959
+Cucumber mosaic virus cucumber mosaic cucumovirus 1 0 VRL 12305
+Cucumis melo muskmelon 1 1 PLN 3656
+Cucumis sativus cucumber 1 1 PLN 3659
+Culex pipiens house mosquito 1 5 INV 7175
+Curculio glandium 1 5 INV 197013
+Cycas rumphii 1 1 PLN 58031
+Cynodon dactylon Bermuda grass 1 1 PLN 28909
+Cyprinus carpio common carp 1 2 VRT 7962
+Daktulosphaira vitifoliae grape phylloxera 1 5 INV 58002
+Danio rerio zebrafish 1 2 VRT 7955
+Dasypus novemcinctus nine-banded armadillo 1 2 MAM 9361
+Daucus carota carrot 1 1 PLN 4039
+Debaryomyces hansenii 1 3 PLN 4959
+Deinococcus radiodurans 11 0 BCT 1299
+Delacroixia coronata 1 4 PLN 34488
+Dendrocopos major 1 2 VRT 137523
+Dengue virus 1 0 VRL 12637
+Descurainia sophia 1 1 PLN 89411
+Desulfitobacterium hafniense 11 0 BCT 49338
+Desulfovibrio desulfuricans 11 0 BCT 876
+Diadema antillarum 1 9 INV 105358
+Dianthus caryophyllus clove pink 1 1 PLN 3570
+Dicentrarchus labrax European sea bass 1 2 VRT 13489
+Dictyostelium discoideum 1 1 INV 44689
+Dirofilaria immitis dog heartworm nematode 1 5 INV 6287
+Dreissena polymorpha 1 5 INV 45954
+Drosophila americana 1 5 INV 40366
+Drosophila ananassae 1 5 INV 7217
+Drosophila buzzatii 1 5 INV 7264
+Drosophila mauritiana 1 5 INV 7226
+Drosophila melanogaster fruit fly 1 5 INV 7227
+Drosophila miranda 1 5 INV 7229
+Drosophila persimilis 1 5 INV 7234
+Drosophila pseudoobscura 1 5 INV 7237
+Drosophila simulans 1 5 INV 7240
+Drosophila subobscura 1 5 INV 7241
+Drosophila virilis 1 5 INV 7244
+Drosophila yakuba 1 5 INV 7245
+Dugesia japonica 1 9 INV 6161
+Dunaliella salina 1 1 PLN 3046
+Echinococcus granulosus 1 9 INV 6210
+Echinococcus multilocularis 1 9 INV 6211
+Echinostoma paraensei 1 14 INV 48215
+Eimeria tenella 1 4 INV 5802
+Elephas maximus Asiatic elephant 1 2 MAM 9783
+Emericella nidulans 1 4 PLN 162425
+Emiliania huxleyi 1 4 PLN 2903
+Entamoeba histolytica 1 1 INV 5759
+Entamoeba invadens 1 1 INV 33085
+Enterobacter cloacae 11 0 BCT 550
+Enterobacteria phage T7 11 0 PHG 10760
+Enterococcus faecalis 11 0 BCT 1351
+Enterococcus faecium 11 0 BCT 1352
+Epinephelus quernus Hawaiian grouper 1 2 VRT 212795
+Equine arteritis virus 1 0 VRL 11047
+Equine infectious anemia virus 1 0 VRL 11665
+Equus caballus horse 1 2 MAM 9796
+Eremothecium gossypii 1 3 PLN 33169
+Erwinia amylovora 11 0 BCT 552
+Escherichia coli 11 0 BCT 562
+Eschscholzia californica California poppy 1 1 PLN 3467
+Eucalyptus globulus 1 1 PLN 34317
+Eucalyptus grandis 1 1 PLN 71139
+Eucalyptus tereticornis 1 1 PLN 183855
+Euhadra peliomphala 1 5 INV 87841
+Eulemur fulvus brown lemur 1 2 PRI 13515
+Euphorbia esula leafy spurge 1 1 PLN 3993
+Euphorbia lagascae 1 1 PLN 54672
+Feline immunodeficiency virus 1 0 VRL 11673
+Feline leukemia virus 1 0 VRL 11768
+Felis catus cat 1 2 MAM 9685
+Ferroplasma acidarmanus 11 0 BCT 97393
+Filobasidiella bacillispora 1 4 PLN 37769
+Filobasidiella neoformans 1 4 PLN 5207
+Foot-and-mouth disease virus A 1 0 VRL 12111
+Foot-and-mouth disease virus O 1 0 VRL 12118
+Fragaria x ananassa 1 1 PLN 3747
+Fragilariopsis cylindrus 1 1 PLN 186039
+Francisella tularensis 11 0 BCT 263
+Fucus distichus 1 1 PLN 3012
+Fugu rubripes 1 2 VRT 31033
+Fundulus heteroclitus killifish 1 2 VRT 8078
+Fusarium oxysporum 1 4 PLN 5507
+Fusarium sporotrichioides 1 4 PLN 5514
+Fusarium subglutinans 1 4 PLN 42677
+Fusobacterium nucleatum 11 0 BCT 851
+Gadus morhua Atlantic cod 1 2 VRT 8049
+Gallus gallus chicken 1 2 VRT 9031
+Gasterosteus aculeatus three spined stickleback 1 2 VRT 69293
+GB virus C/Hepatitis G virus Hepatitis GB virus C / Hepatitis G virus 1 0 VRL 54290
+Geobacillus stearothermophilus 11 0 BCT 1422
+Geobacter metallireducens 11 0 BCT 28232
+Geochelone nigra 1 2 VRT 66189
+Giardia intestinalis 1 0 INV 5741
+Giardia lamblia 1 0 INV 5741
+Gibberella moniliformis 1 4 PLN 117187
+Gibberella zeae 1 4 PLN 5518
+Gillichthys mirabilis long-jawed mudsucker 1 2 VRT 8222
+Ginglymostoma cirratum nurse shark 1 2 VRT 7801
+Ginkgo biloba maidenhair tree 1 1 PLN 3311
+Globodera pallida 1 5 INV 36090
+Globodera rostochiensis 1 5 INV 31243
+Glomerella cingulata 1 4 PLN 5457
+Glomus intraradices 1 4 PLN 4876
+Glomus versiforme 1 4 PLN 43425
+Glossina morsitans 1 5 INV 7394
+Glycine clandestina 1 1 PLN 45687
+Glycine max soybean 1 1 PLN 3847
+Glycine tomentella 1 1 PLN 44015
+Glyphorynchus spirurus wedge-billed woodcreeper 1 2 VRT 135974
+Gnetum gnemon 1 1 PLN 3382
+Gorilla gorilla gorilla 1 2 PRI 9593
+Gossypium arboreum 1 1 PLN 29729
+Gossypium barbadense sea-island cotton 1 1 PLN 3634
+Gossypium herbaceum 1 1 PLN 34274
+Gossypium hirsutum upland cotton 1 1 PLN 3635
+Gossypium raimondii 1 1 PLN 29730
+Gracilaria gracilis 1 4 PLN 2777
+Gregarina niphandrodes 1 4 INV 110365
+Griffithsia japonica 1 1 PLN 83288
+Guillardia theta 1 1 PLN 55529
+Haematobia irritans horn fly 1 5 INV 7368
+Haemonchus contortus 1 5 INV 6289
+Haemophilus influenzae 11 0 BCT 727
+Haloarcula marismortui 11 0 BCT 2238
+Halobacterium sp. NRC-1 11 0 BCT 64091
+Halobaculum gomorrense 11 0 BCT 43928
+Halocynthia roretzi 1 13 INV 7729
+Halorubrum lacusprofundi 11 0 BCT 2247
+Hebeloma cylindrosporum 1 4 PLN 76867
+Hedyotis centranthoides 1 1 PLN 219666
+Hedyotis terminalis 1 1 PLN 219667
+Helianthus annuus common sunflower 1 1 PLN 4232
+Helianthus argophyllus 1 1 PLN 73275
+Helianthus paradoxus 1 1 PLN 73304
+Helicobacter pylori 11 0 BCT 210
+Heliconius melpomene 1 5 INV 34740
+Helicoverpa armigera cotton bollworm 1 5 INV 29058
+Heliocidaris erythrogramma 1 9 INV 7634
+Hemicentrotus pulcherrimus 1 9 INV 7650
+Hepatitis A virus 1 0 VRL 12092
+Hepatitis B virus 1 0 VRL 10407
+Hepatitis C virus 1 0 VRL 11103
+Hepatitis D virus 1 0 VRL 12475
+Hepatitis E virus 1 0 VRL 12461
+Heterobasidion annosum 1 4 PLN 13563
+Heterodera glycines 1 5 INV 51029
+Heterodera schachtii 1 5 INV 97005
+Hevea brasiliensis Para rubber tree 1 1 PLN 3981
+Hippoglossus hippoglossus Atlantic halibut 1 2 VRT 8267
+Histophilus somni 11 0 BCT 731
+Holothuria nobilis 1 9 INV 221420
+Homalodisca coagulata glassy-winged sharpshooter 1 5 INV 197043
+Homo sapiens human 1 2 PRI 9606
+Hordeum vulgare 1 1 PLN 4513
+Human adenovirus B 1 0 VRL 108098
+Human adenovirus C 1 0 VRL 129951
+Human astrovirus 1 0 VRL 12702
+Human endogenous retrovirus 1 0 VRL 11827
+Human enterovirus A 1 0 VRL 138948
+Human enterovirus B 1 0 VRL 138949
+Human enterovirus C 1 0 VRL 138950
+Human herpesvirus 1 1 0 VRL 10298
+Human herpesvirus 3 1 0 VRL 10335
+Human herpesvirus 4 Epstein-Barr virus 1 0 VRL 10376
+Human herpesvirus 5 1 0 VRL 10359
+Human herpesvirus 8 Kaposi's sarcoma-associated herpesvirus - Human herpesvirus 8 1 0 VRL 37296
+Human immunodeficiency virus 1 0 VRL 12721
+Human immunodeficiency virus 1 1 0 VRL 11676
+Human immunodeficiency virus 2 1 0 VRL 11709
+Human papillomavirus 1 0 VRL 10566
+Human papillomavirus type 16 1 0 VRL 10581
+Human respiratory syncytial virus 1 0 VRL 11250
+Hydra magnipapillata 1 4 INV 6085
+Hylobates lar common gibbon 1 2 PRI 9580
+Hypocrea jecorina 1 4 PLN 51453
+Hypocrea lixii 1 4 PLN 5544
+Hypsibius dujardini 1 5 INV 232323
+Ichthyophthirius multifiliis 6 4 INV 5932
+Ictalurus furcatus 1 2 VRT 66913
+Ictalurus punctatus channel catfish 1 2 VRT 7998
+Infectious bursal disease virus Gumboro virus 1 0 VRL 10995
+Infectious salmon anemia virus 1 0 VRL 55987
+Ipomoea batatas sweet potato 1 1 PLN 4120
+Ipomoea nil Japanese morning glory 1 1 PLN 35883
+Ipomoea trifida 1 1 PLN 35884
+Ips pini North American pine engraver 1 5 INV 102803
+Iris hollandica 1 1 PLN 35876
+Isotricha sp. BBF-2003 1 4 INV 223153
+Ixodes scapularis black-legged tick 1 5 INV 6945
+Japanese encephalitis virus 1 0 VRL 11072
+JC virus 1 0 VRL 10632
+Juglans regia English walnut 1 1 PLN 51240
+Kandelia candel 1 1 PLN 61147
+Klebsiella oxytoca 11 0 BCT 571
+Klebsiella pneumoniae 11 0 BCT 573
+Kluyveromyces delphensis 1 3 PLN 51657
+Kluyveromyces lactis 1 3 PLN 28985
+Kluyveromyces marxianus 1 3 PLN 4911
+Kluyveromyces thermotolerans 1 3 PLN 4916
+Laccaria bicolor 1 4 PLN 29883
+Lactobacillus brevis 11 0 BCT 1580
+Lactobacillus delbrueckii 11 0 BCT 1584
+Lactobacillus plantarum 11 0 BCT 1590
+Lactococcus lactis 11 0 BCT 1358
+Lactuca sativa 1 1 PLN 4236
+Lactuca serriola 1 1 PLN 75943
+Lama glama llama 1 2 MAM 9844
+Laminaria digitata 1 1 PLN 80365
+Lawsonia intracellularis 11 0 BCT 29546
+Legionella pneumophila 11 0 BCT 446
+Leifsonia xyli 11 0 BCT 1575
+Leishmania braziliensis 1 4 INV 5660
+Leishmania donovani 1 4 INV 5661
+Leishmania infantum 1 4 INV 5671
+Leishmania major 1 4 INV 5664
+Lemur catta ring-tailed lemur 1 2 PRI 9447
+Leopardus pardalis ocelot 1 2 MAM 32538
+Lepilemur septentrionalis northern sportive lemur 1 2 PRI 78584
+Leptospira interrogans 11 0 BCT 173
+Leuconostoc mesenteroides 11 0 BCT 1245
+Leymus chinensis 1 1 PLN 52714
+Limnanthes alba white meadowfoam 1 1 PLN 42439
+Lingulodinium polyedrum 1 4 PLN 160621
+Linum usitatissimum flax 1 1 PLN 4006
+Listeria innocua 11 0 BCT 1642
+Listeria monocytogenes 11 0 BCT 1639
+Litomosoides sigmodontis 1 5 INV 42156
+Litopenaeus setiferus white shrimp 1 5 INV 64468
+Litopenaeus vannamei Pacific white shrimp 1 5 INV 6689
+Littorina littorea 1 5 INV 31216
+Lotus corniculatus 1 1 PLN 47247
+Loxodonta africana African savanna elephant 1 2 MAM 9785
+Lumbricus rubellus humus earthworm 1 5 INV 35632
+Lupinus albus white lupine 1 1 PLN 3870
+Lupinus luteus yellow lupine 1 1 PLN 3873
+Luscinia svecica 1 2 VRT 52792
+Lutzomyia longipalpis 1 5 INV 7200
+Lycopersicon esculentum tomato 1 1 PLN 4081
+Lycopersicon hirsutum 1 1 PLN 62890
+Lycopersicon pennellii 1 1 PLN 28526
+Macaca fascicularis crab-eating macaque 1 2 PRI 9541
+Macaca fuscata Japanese macaque 1 2 PRI 9542
+Macaca mulatta rhesus monkey 1 2 PRI 9544
+Macaca nemestrina pig-tailed macaque 1 2 PRI 9545
+Macropus eugenii tammar wallaby 1 2 MAM 9315
+Magnaporthe grisea 1 4 PLN 148305
+Magnetococcus sp. MC-1 11 0 BCT 156889
+Magnetospirillum magnetotacticum 11 0 BCT 188
+Malus x domestica apple tree 1 1 PLN 3750
+Manduca sexta tobacco hornworm 1 5 INV 7130
+Manihot esculenta cassava 1 1 PLN 3983
+Marchantia polymorpha liverwort 1 1 PLN 3197
+Marmota monax woodchuck 1 2 ROD 9995
+Marsupenaeus japonicus 1 5 INV 27405
+Martes americana American marten 1 2 MAM 9660
+Mastigamoeba balamuthi 1 1 INV 108607
+Measles virus 1 0 VRL 11234
+Medicago sativa 1 1 PLN 3879
+Medicago truncatula barrel medic 1 1 PLN 3880
+Meladema coriacea 1 5 INV 107907
+Melaleuca alternifolia tea tree 1 1 PLN 164405
+Meleagris gallopavo turkey 1 2 VRT 9103
+Meloidogyne arenaria 1 5 INV 6304
+Meloidogyne chitwoodi 1 5 INV 59747
+Meloidogyne hapla 1 5 INV 6305
+Meloidogyne incognita southern root-knot nematode 1 5 INV 6306
+Meloidogyne javanica root-knot nematode 1 5 INV 6303
+Meloidogyne paranaensis 1 5 INV 189293
+Mentha x piperita peppermint 1 1 PLN 34256
+Meriones unguiculatus Mongolian gerbil 1 2 ROD 10047
+Mesembryanthemum crystallinum common iceplant 1 1 PLN 3544
+Mesobuthus gibbosus 1 5 INV 123226
+Mesocricetus auratus golden hamster 1 2 ROD 10036
+Metarhizium anisopliae 1 4 PLN 5530
+Methanosarcina acetivorans 11 0 BCT 2214
+Methanosarcina barkeri 11 0 BCT 2208
+Methanosarcina mazei 11 0 BCT 2209
+Methanothermobacter thermautotrophicus 11 0 BCT 145262
+Microbotryum violaceum 1 4 PLN 5272
+Microbulbifer degradans 11 0 BCT 86304
+Microcystis aeruginosa 11 0 BCT 1126
+Micromonospora carbonacea 11 0 BCT 47853
+Microtus oeconomus tundra vole 1 2 ROD 64717
+Mnemiopsis leidyi 1 4 INV 27923
+Molgula tectiformis 1 13 INV 30286
+Moneuplotes crassus 10 4 INV 5936
+Monodelphis domestica gray short-tailed opossum 1 2 MAM 13616
+Moraxella catarrhalis 11 0 BCT 480
+Morone saxatilis striped sea-bass 1 2 VRT 34816
+Motacilla flava 1 2 VRT 180448
+Mumps virus 1 0 VRL 11161
+Murine leukemia virus 1 0 VRL 11786
+Mus musculus house mouse 1 2 ROD 10090
+Mus spretus western wild mouse 1 2 ROD 10096
+Musa acuminata 1 1 PLN 4641
+Musca domestica house fly 1 5 INV 7370
+Mycobacterium avium 11 0 BCT 1764
+Mycobacterium bovis 11 0 BCT 1765
+Mycobacterium leprae 11 0 BCT 1769
+Mycobacterium smegmatis 11 0 BCT 1772
+Mycobacterium tuberculosis 11 0 BCT 1773
+Mycoplasma capricolum 4 0 BCT 2095
+Mycoplasma genitalium 4 0 BCT 2097
+Mycoplasma haemofelis 4 0 BCT 29501
+Mycoplasma hominis 4 0 BCT 2098
+Mycosphaerella graminicola 1 4 PLN 54734
+Mystacina tuberculata New Zealand lesser short-tailed bat 1 2 MAM 94961
+Mytilus edulis 1 5 INV 6550
+Mytilus galloprovincialis Mediterranean mussel 1 5 INV 29158
+Mytilus trossulus common blue mussel 1 5 INV 6551
+Myxococcus xanthus 11 0 BCT 34
+Natrialba asiatica 11 0 BCT 64602
+Necator americanus 1 5 INV 51031
+Nectria haematococca 1 4 PLN 140110
+Neisseria gonorrhoeae 11 0 BCT 485
+Neisseria meningitidis 11 0 BCT 487
+Neospora caninum 1 4 INV 29176
+Neospora hughesi 1 4 INV 83675
+Neurospora crassa 1 4 PLN 5141
+Newcastle disease virus 1 0 VRL 11176
+Nicotiana attenuata 1 1 PLN 49451
+Nicotiana benthamiana 1 1 PLN 4100
+Nicotiana sylvestris wood tobacco 1 1 PLN 4096
+Nicotiana tabacum common tobacco 1 1 PLN 4097
+Nippostrongylus brasiliensis 1 5 INV 27835
+Norwalk virus 1 0 VRL 11983
+Nostoc punctiforme 11 0 BCT 63737
+Novosphingobium aromaticivorans 11 0 BCT 48935
+Nuphar advena 1 1 PLN 77108
+Ochrobactrum anthropi 11 0 BCT 529
+Ocinebrellus inornatus Asian drill 1 5 INV 213425
+Oenococcus oeni 11 0 BCT 1247
+Oikopleura dioica 1 5 INV 34765
+Olea europaea common olive 1 1 PLN 4146
+Onchocerca volvulus 1 5 INV 6282
+Oncorhynchus keta chum salmon 1 2 VRT 8018
+Oncorhynchus mykiss rainbow trout 1 2 VRT 8022
+Oncorhynchus nerka sockeye salmon 1 2 VRT 8023
+Oncorhynchus tshawytscha Chinook salmon 1 2 VRT 74940
+Opsanus beta 1 2 VRT 95145
+Oreochromis niloticus Nile tilapia 1 2 VRT 8128
+Ornithodoros porcinus 1 5 INV 34594
+Ornithorhynchus anatinus platypus 1 2 MAM 9258
+Oryctolagus cuniculus rabbit 1 2 MAM 9986
+Oryza minuta 1 1 PLN 63629
+Oryza sativa 1 1 PLN 4530
+Oryzias latipes Japanese medaka 1 2 VRT 8090
+Ostertagia ostertagi 1 5 INV 6317
+Ostreococcus tauri 1 1 PLN 70448
+Otis tarda 1 2 VRT 73107
+Ovis aries sheep 1 2 MAM 9940
+Oxytricha trifallax 6 4 INV 94289
+Pacifastacus leniusculus signal crayfish 1 5 INV 6720
+Pan paniscus pygmy chimpanzee 1 2 PRI 9597
+Pan troglodytes chimpanzee 1 2 PRI 9598
+Panax ginseng 1 1 PLN 4054
+Pantoea agglomerans 11 0 BCT 549
+Papio anubis olive baboon 1 2 PRI 9555
+Papio hamadryas hamadryas baboon 1 2 PRI 9557
+Paracoccidioides brasiliensis 1 4 PLN 121759
+Paralichthys olivaceus bastard halibut 1 2 VRT 8255
+Paramecium tetraurelia 6 4 INV 5888
+Parastrongyloides trichosuri 1 5 INV 131310
+Parus major 1 2 VRT 9157
+Pasteurella multocida 11 0 BCT 747
+Pasteuria penetrans 11 0 BCT 86005
+Paxillus involutus 1 4 PLN 71150
+Pectobacterium atrosepticum 11 0 BCT 29471
+Pectobacterium carotovorum 11 0 BCT 554
+Pediculus humanus human lice 1 5 INV 121225
+Penaeus monodon black tiger shrimp 1 5 INV 6687
+Penicillium marneffei 1 4 PLN 37727
+Pennisetum ciliare buffelgrass 1 1 PLN 35520
+Pennisetum glaucum 1 1 PLN 4543
+Peromyscus leucopus white-footed mouse 1 2 ROD 10041
+Peromyscus maniculatus deer mouse 1 2 ROD 10042
+Pestivirus type 1 1 0 VRL 11099
+Pestivirus type 2 1 0 VRL 54314
+Petromyzon marinus sea lamprey 1 2 VRT 7757
+Petunia x hybrida 1 1 PLN 4102
+Phaeodactylum tricornutum 1 1 PLN 2850
+Phanerochaete chrysosporium 1 4 PLN 5306
+Phaseolus coccineus 1 1 PLN 3886
+Phaseolus vulgaris 1 1 PLN 3885
+Phoca vitulina harbor seal 1 2 MAM 9720
+Photorhabdus luminescens 11 0 BCT 29488
+Physcomitrella patens 1 1 PLN 3218
+Phytophthora infestans potato late blight agent 1 1 PLN 4787
+Phytophthora nicotianae 1 1 PLN 4790
+Phytophthora sojae 1 1 PLN 67593
+Picea abies Norway spruce 1 1 PLN 3329
+Pichia angusta 1 3 PLN 4905
+Pichia farinosa 1 3 PLN 4920
+Pinus pinaster 1 1 PLN 71647
+Pinus radiata Monterey pine 1 1 PLN 3347
+Pinus taeda loblolly pine 1 1 PLN 3352
+Pisolithus microcarpus 1 4 PLN 178872
+Pisolithus tinctorius 1 4 PLN 37468
+Pisum sativum pea 1 1 PLN 3888
+Planococcus lilacinus lilac mealybug 1 5 INV 40930
+Plasmodium berghei 1 4 INV 5821
+Plasmodium chabaudi 1 4 INV 5825
+Plasmodium falciparum malaria parasite P. falciparum 1 4 INV 5833
+Plasmodium vivax malaria parasite P. vivax 1 4 INV 5855
+Plasmodium yoelii 1 4 INV 5861
+Platichthys flesus European flounder 1 2 VRT 8260
+Platystomus albinus 1 5 INV 197009
+Plethodon elongatus Del Norte salamander 1 2 VRT 46761
+Pleuronectes platessa plaice 1 2 VRT 8262
+Pleurotus ostreatus oyster mushroom 1 4 PLN 5322
+Plumbago zeylanica 1 1 PLN 76149
+Pneumocystis carinii 1 4 PLN 4754
+Podarcis hispanica 1 2 VRT 74081
+Poecilia reticulata guppy 1 2 VRT 8081
+Poliovirus 1 0 VRL 138953
+Polyandrocarpa misakiensis 1 13 INV 7723
+Poncirus trifoliata 1 1 PLN 37690
+Pongo pygmaeus orangutan 1 2 PRI 9600
+Populus alba x Populus glandulosa 1 1 PLN 153471
+Populus alba x Populus tremula 1 1 PLN 80863
+Populus balsamifera 1 1 PLN 73824
+Populus balsamifera subsp. trichocarpa x Populus deltoides 1 1 PLN 3695
+Populus tremula 1 1 PLN 113636
+Populus tremula x Populus tremuloides 1 1 PLN 47664
+Populus tremuloides quaking aspen 1 1 PLN 3693
+Porcine reproductive and respiratory syndrome virus 1 0 VRL 28344
+Porphyra yezoensis 1 4 PLN 2788
+Porphyromonas gingivalis 11 0 BCT 837
+Potato virus Y 1 0 VRL 12216
+Pratylenchus penetrans 1 5 INV 45929
+Primate T-lymphotropic virus 1 1 0 VRL 194440
+Primate T-lymphotropic virus 2 1 0 VRL 194441
+Pristionchus pacificus 1 5 INV 54126
+Prunus armeniaca apricot 1 1 PLN 36596
+Prunus dulcis almond 1 1 PLN 3755
+Prunus persica peach 1 1 PLN 3760
+Pseudomonas aeruginosa 11 0 BCT 287
+Pseudomonas fluorescens 11 0 BCT 294
+Pseudomonas putida 11 0 BCT 303
+Pseudomonas stutzeri 11 0 BCT 316
+Pseudomonas syringae 11 0 BCT 317
+Pseudopleuronectes americanus winter flounder 1 2 VRT 8265
+Pseudotsuga menziesii Douglas fir 1 1 PLN 3357
+Psoroptes equi var. ovis sheep scab mite 1 5 INV 83912
+Psoroptes ovis sheep scab mite 1 5 INV 83912
+Pygoscelis adeliae Adelie penguin 1 2 VRT 9238
+Pyricularia grisea 1 4 PLN 148305
+Pyrobaculum aerophilum 11 0 BCT 13773
+Pyrococcus furiosus 11 0 BCT 2261
+Pyrocoelia rufa 1 5 INV 71223
+Pyrocystis lunula 1 4 PLN 2972
+Pyrus communis pear 1 1 PLN 23211
+Rabies virus 1 0 VRL 11292
+Ralstonia metallidurans 11 0 BCT 119219
+Ralstonia solanacearum 11 0 BCT 305
+Rana catesbeiana bullfrog 1 2 VRT 8400
+Rangifer tarandus reindeer 1 2 MAM 9870
+Raphanus sativus radish 1 1 PLN 3726
+Rattus norvegicus Norway rat 1 2 ROD 10116
+Rattus rattus black rat 1 2 ROD 10117
+Respiratory syncytial virus 1 0 VRL 12814
+Rhagoletis pomonella apple maggot 1 5 INV 28610
+Rhinolophus ferrumequinum greater horseshoe bat 1 2 MAM 59479
+Rhizobium etli 11 0 BCT 29449
+Rhizobium leguminosarum 11 0 BCT 384
+Rhizobium meliloti 11 0 BCT 382
+Rhizobium radiobacter 11 0 BCT 358
+Rhizobium sp. NGR234 11 0 BCT 394
+Rhizoctonia solani 1 4 PLN 107832
+Rhodobacter sphaeroides 11 0 BCT 1063
+Rhodococcus erythropolis 11 0 BCT 1833
+Rhodospirillum rubrum 11 0 BCT 1085
+Rhopalosiphum padi bird cherry-oat aphid 1 5 INV 40932
+Ricinus communis castor bean 1 1 PLN 3988
+Rickettsia prowazekii 11 0 BCT 782
+Robinia pseudoacacia 1 1 PLN 35938
+Rosa chinensis 1 1 PLN 74649
+Rosa hybrid cultivar 1 1 PLN 128735
+Rotavirus A 1 0 VRL 28875
+Rous sarcoma virus 1 0 VRL 11886
+Rubella virus 1 0 VRL 11041
+Ruminococcus flavefaciens 11 0 BCT 1265
+Saccharomyces bayanus 1 3 PLN 4931
+Saccharomyces cariocanus 1 3 PLN 114526
+Saccharomyces castellii 1 3 PLN 27288
+Saccharomyces cerevisiae baker's yeast 1 3 PLN 4932
+Saccharomyces exiguus 1 3 PLN 34358
+Saccharomyces kluyveri 1 3 PLN 4934
+Saccharomyces kudriavzevii 1 3 PLN 114524
+Saccharomyces mikatae 1 3 PLN 114525
+Saccharomyces paradoxus 1 3 PLN 27291
+Saccharomyces servazzii 1 3 PLN 27293
+Saccharomyces unisporus 1 3 PLN 27294
+Saccharum officinarum 1 1 PLN 4547
+Saguinus oedipus cotton-top tamarin 1 2 PRI 9490
+Saimiri sciureus common squirrel monkey 1 2 PRI 9521
+Salix viminalis osier 1 1 PLN 40686
+Salmo salar Atlantic salmon 1 2 VRT 8030
+Salmo trutta brown trout 1 2 VRT 8032
+Salmonella enterica 11 0 BCT 28901
+Salmonella typhimurium 11 0 BCT 602
+Salvelinus alpinus Arctic char 1 2 VRT 8036
+Sarcocystis neurona 1 4 INV 42890
+Sarcoptes scabiei 1 5 INV 52283
+Scherffelia dubia 1 1 PLN 3190
+Schistosoma japonicum 1 9 INV 6182
+Schistosoma mansoni 1 9 INV 6183
+Schizophyllum commune 1 4 PLN 5334
+Schizosaccharomyces pombe fission yeast 1 4 PLN 4896
+Schmidtea mediterranea 1 9 INV 79327
+Sciaenops ocellatus 1 2 VRT 76340
+Sclerotinia sclerotiorum 1 4 PLN 5180
+Sebastes mystinus 1 2 VRT 72088
+Secale cereale rye 1 1 PLN 4550
+Selaginella lepidophylla 1 1 PLN 59777
+SEN virus 1 0 VRL 136966
+Seriola quinqueradiata five-ray yellowtail 1 2 VRT 8161
+Serratia marcescens 11 0 BCT 615
+Sesamum indicum sesame 1 1 PLN 4182
+Sesbania rostrata 1 1 PLN 3895
+Shewanella oneidensis 11 0 BCT 70863
+Shigella flexneri 11 0 BCT 623
+Shrimp white spot syndrome virus 1 0 VRL 92652
+Silene latifolia 1 1 PLN 37657
+Silurana tropicalis western clawed frog 1 2 VRT 8364
+Simian immunodeficiency virus 1 0 VRL 11723
+Simian virus 40 1 0 VRL 10633
+Simian-Human immunodeficiency virus 1 0 VRL 57667
+Sindbis virus 1 0 VRL 11034
+Sinorhizobium meliloti 11 0 BCT 382
+Solanum tuberosum potato 1 1 PLN 4113
+Sorghum bicolor sorghum 1 1 PLN 4558
+Sorghum halepense 1 1 PLN 4560
+Sorghum propinquum 1 1 PLN 132711
+Sparus aurata gilthead seabream 1 2 VRT 8175
+Sphingomonas aromaticivorans 11 0 BCT 48935
+Spinacia oleracea spinach 1 1 PLN 3562
+Spiroplasma kunkelii 4 0 BCT 47834
+Sporotrichum pruinosum 1 4 PLN 5306
+Staphylococcus aureus 11 0 BCT 1280
+Staphylococcus epidermidis 11 0 BCT 1282
+Stealth virus 1 1 0 VRL 36452
+Sterkiella histriomuscorum 6 4 INV 94289
+Stevia rebaudiana 1 1 PLN 55670
+Streptococcus agalactiae 11 0 BCT 1311
+Streptococcus dysgalactiae 11 0 BCT 1334
+Streptococcus equi 11 0 BCT 1336
+Streptococcus mitis 11 0 BCT 28037
+Streptococcus mutans 11 0 BCT 1309
+Streptococcus oralis 11 0 BCT 1303
+Streptococcus pneumoniae 11 0 BCT 1313
+Streptococcus pyogenes 11 0 BCT 1314
+Streptococcus suis 11 0 BCT 1307
+Streptococcus thermophilus 11 0 BCT 1308
+Streptomyces coelicolor 11 0 BCT 1902
+Streptomyces lividans 11 0 BCT 1916
+Strongylocentrotus purpuratus 1 9 INV 7668
+Strongyloides ratti 1 5 INV 34506
+Strongyloides stercoralis 1 5 INV 6248
+Struthio camelus ostrich 1 2 VRT 8801
+Suaeda maritima 1 1 PLN 126913
+Suid herpesvirus 1 1 0 VRL 10345
+Sulfolobus solfataricus 11 0 BCT 2287
+Sus scrofa pig 1 2 MAM 9823
+Symsagittifera roscofensis 1 5 INV 84072
+Syncerus caffer African buffalo 1 2 MAM 9970
+Tadarida brasiliensis Brazilian free-tailed bat 1 2 MAM 9438
+Taenia solium pork tapeworm 1 9 INV 6204
+Takifugu rubripes 1 2 VRT 31033
+Tamarix androssowii 1 1 PLN 189785
+Tamias amoenus yellow-pine chipmunk 1 2 ROD 64679
+Tamias ruficaudus red-tailed chipmunk 1 2 ROD 123792
+Teladorsagia circumcincta 1 5 INV 45464
+Telestes souffia 1 2 VRT 129883
+Tetrahymena thermophila 6 4 INV 5911
+Tetraodon nigroviridis 1 2 VRT 99883
+Thanatephorus cucumeris 1 4 PLN 107832
+Theileria parva 1 4 INV 5875
+Thellungiella halophila 1 1 PLN 98038
+Theobroma cacao cacao 1 1 PLN 3641
+Thermoanaerobacter tengcongensis 11 0 BCT 119072
+Thermotoga maritima 11 0 BCT 2336
+Thermotoga sp. RQ2 11 0 BCT 126740
+Thermus thermophilus 11 0 BCT 274
+Timarcha balearica 1 5 INV 79517
+Toxocara canis 1 5 INV 6265
+Toxoplasma gondii 1 4 INV 5811
+Toxoptera citricida brown citrus aphid 1 5 INV 223852
+Toxostoma curvirostre 1 2 VRT 99878
+Treponema pallidum 11 0 BCT 160
+Tribolium castaneum red flour beetle 1 5 INV 7070
+Trichinella spiralis 1 5 INV 6334
+Trichoderma harzianum 1 4 PLN 5544
+Trichoderma reesei 1 4 PLN 51453
+Trichodesmium erythraeum 11 0 BCT 1206
+Trichomonas vaginalis 1 0 INV 5722
+Trichoplusia ni cabbage looper 1 5 INV 7111
+Trichostrongylus vitrinus 1 5 INV 40352
+Trichosurus vulpecula silver-gray brushtail possum 1 2 MAM 9337
+Trichuris muris 1 5 INV 70415
+Trichuris vulpis 1 5 INV 219738
+Trifolium repens white clover 1 1 PLN 3899
+Triphysaria versicolor 1 1 PLN 64093
+Triticum aestivum bread wheat 1 1 PLN 4565
+Triticum monococcum 1 1 PLN 4568
+Triticum turgidum 1 1 PLN 4571
+Tropheus moorii blunthead cichlid 1 2 VRT 8150
+Trypanosoma brucei 1 4 INV 5691
+Trypanosoma carassii 1 4 INV 38249
+Trypanosoma cruzi 1 4 INV 5693
+TT virus 1 0 VRL 68887
+TTV-like mini virus 1 0 VRL 93678
+Tuber borchii whitish truffle 1 4 PLN 42251
+Turkey rhinotracheitis virus 1 0 VRL 11264
+Turnip mosaic virus 1 0 VRL 12230
+Ureaplasma urealyticum 4 0 BCT 2130
+Ursus arctos brown bear 1 2 MAM 9644
+Ustilago maydis 1 4 PLN 5270
+Vaccinia virus 1 0 VRL 10245
+Vaccinium corymbosum 1 1 PLN 69266
+Verticillium dahliae 1 4 PLN 27337
+Vesicular stomatitis virus 1 0 VRL 11276
+Vibrio cholerae 11 0 BCT 666
+Vibrio parahaemolyticus 11 0 BCT 670
+Vibrio vulnificus 11 0 BCT 672
+Vicia faba fava bean 1 1 PLN 3906
+Vigna radiata 1 1 PLN 157791
+Vigna unguiculata cowpea 1 1 PLN 3917
+Vitis aestivalis 1 1 PLN 3605
+Vitis hybrid cultivar 1 1 PLN 241073
+Vitis riparia 1 1 PLN 96939
+Vitis shuttleworthii 1 1 PLN 246827
+Vitis vinifera 1 1 PLN 29760
+West Nile virus 1 0 VRL 11082
+Wuchereria bancrofti 1 5 INV 6293
+Xanthomonas axonopodis 11 0 BCT 53413
+Xanthomonas campestris 11 0 BCT 339
+Xenopus laevis African clawed frog 1 2 VRT 8355
+Xenopus tropicalis western clawed frog 1 2 VRT 8364
+Xiphias gladius swordfish 1 2 VRT 8245
+Xylella fastidiosa 11 0 BCT 2371
+Yarrowia lipolytica 1 3 PLN 4952
+Yersinia enterocolitica 11 0 BCT 630
+Yersinia pestis 11 0 BCT 632
+Zamia furfuracea 1 1 PLN 42329
+Zea mays 1 1 PLN 4577
+Zeldia punctata 1 5 INV 49351
+Zinnia elegans 1 1 PLN 34245
+Zucchini yellow mosaic virus 1 0 VRL 12232
+Zygosaccharomyces rouxii 1 3 PLN 4956
--- /dev/null
+%
+% New matrix
+%
+% weighted
+w 14 1.89 0.30 1.04 0.27 20
+w 21 1.79 0.24 0.92 0.22 25
+w 28 1.74 0.20 0.86 0.18 30
+uw 14 1.82 0.28 0.95 0.26 20
+uw 21 1.74 0.23 0.86 0.21 25
+uw 28 1.69 0.18 0.80 0.18 30
+%
+% a b c d e f g
+L 2.998 0.269 0.367 3.852 0.510 0.514 0.562
+I 2.408 0.261 0.345 0.931 0.402 0.440 0.289
+V 1.525 0.479 0.350 0.887 0.286 0.350 0.362
+M 2.161 0.605 0.442 1.441 0.607 0.457 0.570
+F 0.490 0.075 0.391 0.639 0.125 0.081 0.038
+Y 1.319 0.064 0.081 1.526 0.204 0.118 0.096
+G 0.084 0.215 0.432 0.111 0.153 0.367 0.125
+A 1.283 1.364 1.077 2.219 0.490 1.265 0.903
+K 1.233 2.194 1.817 0.611 2.095 1.686 2.027
+R 1.014 1.476 1.771 0.114 1.667 2.006 1.844
+H 0.590 0.646 0.584 0.842 0.307 0.611 0.396
+E 0.281 3.351 2.998 0.789 4.868 2.735 3.812
+D 0.068 2.103 1.646 0.182 0.664 1.581 1.401
+Q 0.311 2.290 2.330 0.811 2.596 2.155 2.585
+N 1.231 1.683 2.157 0.197 1.653 2.430 2.065
+S 0.332 0.753 0.930 0.424 0.734 0.801 0.518
+T 0.197 0.543 0.647 0.680 0.905 0.643 0.808
+C 0.918 0.002 0.385 0.440 0.138 0.432 0.079
+W 0.066 0.064 0.065 0.747 0.006 0.115 0.014
+P 0.004 0.108 0.018 0.006 0.010 0.004 0.007
+%
git://source.jalview.org / jpred.git / commitdiff