From cf835f540a5e3f9ccf8cdcd550d24e013db46486 Mon Sep 17 00:00:00 2001 From: Sasha Sherstnev Date: Fri, 13 Sep 2013 15:47:42 +0100 Subject: [PATCH] Add SS prediction for multiple aligment into jpred.pl. Before this was a part of another script --- binaries/src/jpred/jpred.pl | 687 ++++++++++++++++-------- binaries/src/jpred/lib/Paths.pm | 10 +- binaries/src/jpred/tests/alignment.clustal | 186 +++++++ binaries/src/jpred/tests/alignment.fasta | 267 +++++++++ binaries/src/jpred/tests/alignment.msf | 372 +++++++++++++ binaries/src/jpred/tests/d1b3aa_.fas | 2 + binaries/src/jpred/tests/res_d16vpa_.align | 78 --- binaries/src/jpred/tests/res_d16vpa_.concise | 25 - binaries/src/jpred/tests/res_d16vpa_.hmm | 356 ------------ binaries/src/jpred/tests/res_d16vpa_.jnet | 12 - binaries/src/jpred/tests/res_d16vpa_.profile | 365 ------------- binaries/src/jpred/tests/res_d16vpa_.pssm | 356 ------------ binaries/src/jpred/tests/res_d16vpa_.res | 114 ---- binaries/src/jpred/tests/res_d16vpa_.res.fasta | 114 ---- binaries/src/jpred/tests/todo.bash | 12 +- binaries/src/jpred/x86_64/alscript | Bin 0 -> 93595 bytes binaries/src/jpred/x86_64/readseq | Bin 0 -> 62470 bytes 17 files changed, 1295 insertions(+), 1661 deletions(-) create mode 100644 binaries/src/jpred/tests/alignment.clustal create mode 100644 binaries/src/jpred/tests/alignment.fasta create mode 100644 binaries/src/jpred/tests/alignment.msf create mode 100644 binaries/src/jpred/tests/d1b3aa_.fas delete mode 100644 binaries/src/jpred/tests/res_d16vpa_.align delete mode 100644 binaries/src/jpred/tests/res_d16vpa_.concise delete mode 100644 binaries/src/jpred/tests/res_d16vpa_.hmm delete mode 100644 binaries/src/jpred/tests/res_d16vpa_.jnet delete mode 100644 binaries/src/jpred/tests/res_d16vpa_.profile delete mode 100644 binaries/src/jpred/tests/res_d16vpa_.pssm delete mode 100644 binaries/src/jpred/tests/res_d16vpa_.res delete mode 100644 binaries/src/jpred/tests/res_d16vpa_.res.fasta create mode 100755 binaries/src/jpred/x86_64/alscript create mode 100755 binaries/src/jpred/x86_64/readseq diff --git a/binaries/src/jpred/jpred.pl b/binaries/src/jpred/jpred.pl index 74206dd..f5910fc 100755 --- a/binaries/src/jpred/jpred.pl +++ b/binaries/src/jpred/jpred.pl @@ -6,23 +6,26 @@ jpred - Secondary structure prediction program =head1 SYNOPSIS -./jpred.pl -in/-sequence [-outfile ] [-logfile ] [-output ] [-dbname ] [-dbpath ] [-ncpu NNN] [-psi ] [-pred-nohits] [-no-final] [-jabaws] [-verbose] [-debug] [-help] [-man] +./jpred.pl -in [-outfile ] [-logfile ] [-output ] [-dbname ] [-dbpath ] [-ncpu NNN] [-psi ] [-seq] [-pred-nohits] [-no-final] [-jabaws] [-verbose] [-debug] [-help] [-man] =head1 DESCRIPTION -This is a program which predicts the secondary structure of a protein sequence given a path to a -FASTA sequence. It does all the PSI-BLAST searching and alignment 'meddling' as required by Jnet. - -The program is primarily design for use by the Jpred server, but it can be used directly by any user. -Some of the output may not be meaningful if used directly - it can be safely ignored. +This is a program for predicting the secondary structure of a multiple sequence alignment (by default) or a protein sequence +(with the -seq option). The input file can be stored in 3 formats: FASTA, MSF, or BLC. +For the single sequence the program does all the PSI-BLAST searching, preparing PSSM and HMM profiles and predicting the +secondary structure with Jnet. For the multiple sequence alignment only the HMM profile, created from the alignment, is used in Jnet. =head1 OPTIONS =over 5 -=item -in/-sequence +=item -in + +The path to the sequence file (in FASTA, MSF, or BLC format) -The path to the sequence file (in FASTA format) you want to predict. +=item -seq + +The input file is a FASTA file with one sequence only. =item -output @@ -112,15 +115,13 @@ use Carp; use Data::Dumper; use File::Temp; -#use UNIVERSAL; - # path to Jpred modules use FindBin qw($Bin); use lib "$Bin/lib"; # internal jpred modules use Jpred; -use Paths qw($pairwise $oc $jnet $hmmbuild $hmmconvert $psiblastbin check_OS setup_env); +use Paths qw($pairwise $oc $jnet $hmmbuild $hmmconvert $psiblastbin $alscript $readseq check_OS setup_env); use HMMER::Profile; use HMMER::Profile::Jnet; use PSIBLAST; @@ -182,13 +183,17 @@ our $GAP = '-'; ##################################################################################################### my $infile; +my $infastafile; +my $format; +my $goal = "align"; +my $seqgoal; my $outfile; my $prefix; my $psiblast; my $jabaws; my $logfile; -my $ncpu = 1; # number of CPUs for psiblast calculations -my $predNoHits = 0; # define whether to make predictions when no PSI-BLAST hits are found +my $ncpu = 1; # number of CPUs for psiblast calculations +my $predNoHits = 0; # define whether to make predictions when no PSI-BLAST hits are found my $db_path = "/homes/www-jpred/databases"; my $db_entry = "cluster"; my $nofinal; @@ -196,30 +201,34 @@ my $nofinal; my ( $help, $man, $DEBUG, $VERBOSE ); GetOptions( - "in|sequence=s" => \$infile, - "output=s" => \$prefix, - "outfile=s" => \$outfile, - "logfile=s" => \$logfile, - "psi=s" => \$psiblast, - "dbname=s" => \$db_entry, - "dbpath=s" => \$db_path, - "ncpu=s" => \$ncpu, - "pred-nohits" => \$predNoHits, - "no-final" => \$nofinal, - "jabaws" => \$jabaws, - "help" => \$help, - "man" => \$man, - "debug" => \$DEBUG, - "verbose" => \$VERBOSE + "in=s" => \$infile, + "output=s" => \$prefix, + "outfile=s" => \$outfile, + "logfile=s" => \$logfile, + "psi=s" => \$psiblast, + "dbname=s" => \$db_entry, + "dbpath=s" => \$db_path, + "ncpu=s" => \$ncpu, + "pred-nohits" => \$predNoHits, + "no-final" => \$nofinal, + "seq" => \$seqgoal, + "jabaws" => \$jabaws, + + "help" => \$help, + "man" => \$man, + "debug" => \$DEBUG, + "verbose" => \$VERBOSE ) or pod2usage(2); pod2usage(1) if $help; pod2usage( verbose => 2 ) if $man; +$goal = "seq" if ( defined $seqgoal ); + ##################################################################################################### # Key to database information and information for accessing them -if (defined $jabaws) { - $db_path = "/data/UNIREFdb"; - $db_entry = "cluster"; +if ( defined $jabaws ) { + $db_path = "/data/UNIREFdb"; + $db_entry = "cluster"; } my $database = { @@ -270,22 +279,24 @@ my $database = { }; my $dp = $database->{$db_entry}{database}; -pod2usage("ERROR! Input file with a sequence should be provided with -sequence/-in") unless $infile; -pod2usage("ERROR! Unknown database at $db_path. Use -dbpath and -dbname for configuring the database" ) unless exists $database->{$db_entry}; +pod2usage("ERROR! Input file should be provided with -sequence/-in") unless $infile; +pod2usage("ERROR! Unknown database at $db_path. Use -dbpath and -dbname for configuring the database") unless exists $database->{$db_entry}; pod2usage("ERROR! UNIREF database is not available at $dp. Use -dbpath and -dbname for configuring the database") unless -f $dp; +##################################################################################################### +# lots of preparation steps if ( defined $prefix ) { - unless (defined $outfile) { - $outfile = $prefix. ".res.fasta"; + unless ( defined $outfile ) { + $outfile = $prefix . ".res.fasta"; } } else { - if (defined $outfile) { + if ( defined $outfile ) { print "WARNING! file prefix is not defined. Jpred will use $outfile.tmp as the prefix\n"; $prefix = $outfile . ".tmp"; } else { print "WARNING! file prefix is not defined. Jpred will use $infile.res as the prefix\n"; - $prefix = $infile . ".res"; - $outfile = $prefix. ".jnet"; + $prefix = $infile . ".res"; + $outfile = $prefix . ".jnet"; } } @@ -297,7 +308,7 @@ if ( 1 > $ncpu or 8 < $ncpu ) { $VERBOSE = 1 if $DEBUG; my $LOG; -if (defined $logfile) { +if ( defined $logfile ) { open( $LOG, ">", $logfile ) or die "ERROR! unable to open '$logfile': ${!}\nDied"; } @@ -309,8 +320,7 @@ for ( [ "input file", $infile ], [ "out file", $outfile ], [ "outprefix", $prefi print $LOG "$par\n" if $LOG; } -##################################################################################################### -if (defined $jabaws) { +if ( defined $jabaws ) { setup_jpred_env($Bin); setup_env($Bin); } @@ -319,215 +329,269 @@ print "JPRED: checking platiform... $platform\n" if $DEBUG; print $LOG "JPRED: checking platiform... $platform\n" if $LOG; ##################################################################################################### -my $query = FASTA::File->new( read_file => $infile ); - -my @seqs; -my $psi = PSIBLAST->new; -unless ( defined $psiblast && -e $psiblast ) { - ## potentially a better set of parameters (esp. -b & -v) which avoid PSI-BLAST dying with large number of hits - # args => '-e0.05 -h0.01 -m6 -b10000 -v10000 -j3 -F "m S"' # 'soft' filtering of the query sequence - # args => '-e0.001 -h0.0001 -m6 -b10000 -v10000 -j3' # stricter searching criteria - # args => '-e0.05 -h0.01 -m6 -b10000 -v10000 -j3' - my $psi_run = PSIBLAST::Run->new( - debug => $DEBUG, - args => "-a" . $ncpu . " -e0.05 -h0.01 -m6 -b10000 -v10000 -j3", - path => $psiblastbin, - input => $infile, - output => "$prefix.blast", - matrix => "$prefix.profile", - database => $database->{$db_entry}{database}, - ); - - # For reduced databases, get the size of the orginal and use this as - # the equivilent DB size - if ( $db_entry =~ /^sp_red_/ ) { - ( my $entry = $db_entry ) =~ s/^sp_red_/sp_/; - $psi_run->args( - $psi_run->args . " -z " . fasta_seq_length( $database->{$entry}{database} ) # CC sub is below - ); +# check input file format +if ( 'seq' eq $goal ) { + $format = "seq"; + if ( 1 != check_FASTA_format($infile) ) { + die "\nERROR! jpred requires 1 sequence in the FASTA file if the option -seq used. exit\n"; } - print "BLAST matrix: $ENV{BLASTMAT}\n" if $DEBUG; - print "BLASTDB path: $ENV{BLASTDB}\n" if $DEBUG; - print $LOG "BLAST matrix: $ENV{BLASTMAT}\n" if $LOG; - print $LOG "BLASTDB path: $ENV{BLASTDB}\n" if $LOG; - - print "Running PSI-BLAST on query against \'$database->{$db_entry}{database}\'...\n" if $VERBOSE; - print $LOG "Running PSI-BLAST on query against \'$database->{$db_entry}{database}\'...\n" if $LOG; - $psi_run->run or die; # CC sub is from PSIBLAST::Run - - $psi->read_file("$prefix.blast"); # CC PSIBLAST.pm doesn't have a read_file(), but Read.pm does? - system("gzip -9f $prefix.blast"); } else { - if ( $psiblast =~ /.gz$/ ) { $psi->read_gzip_file($psiblast) } # CC PSIBALST.pm doesn't have a read_gzip_file() object, but Read.pm does? - else { $psi->read_file($psiblast) } # CC ditto above + my $nseq = check_FASTA_format($infile); + if ( 0 < $nseq ) { + $format = "fasta"; + if ( 1 == $nseq ) { + die "\nERROR! jpred requires alignment with more than 1 sequence\n if you provide only one sequence use the -seq option.\n"; + } + } elsif ( 0 < check_MSF_format($infile) ) { + $format = "msf"; + } elsif ( 0 < check_BLC_format($infile) ) { + $format = "blc"; + } else { + die "ERROR! unknown input file format for multiple sequence alignment (can be FASTA, MSF, or BLC). exit...\n"; + } } +$infastafile = $infile . ".fasta" if ( 'msf' eq $format or 'blc' eq $format ); ##################################################################################################### -# Convert the last itteration into a collection of PSISEQ objects -for ( $psi->get_all ) { # CC sub is from PSIBLAST.pm - my ( $id, $start, $align ) = @{$_}; - push @seqs, - PSISEQ->new( - id => $id, - start => $start, - align => [ split( //, $align ) ] +if ( 'seq' eq $goal ) { + my $query = FASTA::File->new( read_file => $infile ); + my @seqs; + my $psi = PSIBLAST->new; + unless ( defined $psiblast && -e $psiblast ) { + ## potentially a better set of parameters (esp. -b & -v) which avoid PSI-BLAST dying with large number of hits + # args => '-e0.05 -h0.01 -m6 -b10000 -v10000 -j3 -F "m S"' # 'soft' filtering of the query sequence + # args => '-e0.001 -h0.0001 -m6 -b10000 -v10000 -j3' # stricter searching criteria + # args => '-e0.05 -h0.01 -m6 -b10000 -v10000 -j3' + my $psi_run = PSIBLAST::Run->new( + debug => $DEBUG, + args => "-a" . $ncpu . " -e0.05 -h0.01 -m6 -b10000 -v10000 -j3", + path => $psiblastbin, + input => $infile, + output => "$prefix.blast", + matrix => "$prefix.profile", + database => $database->{$db_entry}{database}, ); -} + + # For reduced databases, get the size of the orginal and use this as + # the equivilent DB size + if ( $db_entry =~ /^sp_red_/ ) { + ( my $entry = $db_entry ) =~ s/^sp_red_/sp_/; + $psi_run->args( + $psi_run->args . " -z " . fasta_seq_length( $database->{$entry}{database} ) # CC sub is below + ); + } + print "BLAST matrix: $ENV{BLASTMAT}\n" if $DEBUG; + print "BLASTDB path: $ENV{BLASTDB}\n" if $DEBUG; + print $LOG "BLAST matrix: $ENV{BLASTMAT}\n" if $LOG; + print $LOG "BLASTDB path: $ENV{BLASTDB}\n" if $LOG; + + print "Running PSI-BLAST on query against \'$database->{$db_entry}{database}\'...\n" if $VERBOSE; + print $LOG "Running PSI-BLAST on query against \'$database->{$db_entry}{database}\'...\n" if $LOG; + $psi_run->run or die; # CC sub is from PSIBLAST::Run + + $psi->read_file("$prefix.blast"); # CC PSIBLAST.pm doesn't have a read_file(), but Read.pm does? + system("gzip -9f $prefix.blast"); + } else { + if ( $psiblast =~ /.gz$/ ) { $psi->read_gzip_file($psiblast) } # CC PSIBALST.pm doesn't have a read_gzip_file() object, but Read.pm does? + else { $psi->read_file($psiblast) } # CC ditto above + } + +##################################################################################################### + # Convert the last itteration into a collection of PSISEQ objects + for ( $psi->get_all ) { # CC sub is from PSIBLAST.pm + my ( $id, $start, $align ) = @{$_}; + push @seqs, + PSISEQ->new( + id => $id, + start => $start, + align => [ split( //, $align ) ] + ); + } ##################################################################################################### -## When there are no PSI-BLAST hits generate an HMM from the query -## and run Jnet against that only. -## Accuracy won't be as good, but at least it's a prediction -if ( @seqs == 0 ) { - if ( $predNoHits == 0 ) { - warn "\nJPRED: Warning! no PSI-BLAST hits found and '-pred-nohits' option not set. Exiting...\n"; - print ">>100% complete\n"; - print $LOG "\nJPRED: Warning! no PSI-BLAST hits found and '-pred-nohits' option not set. Exiting...\n" if $LOG; - print $LOG ">>100% complete\n" if $LOG; - close ($LOG) if $LOG; - exit; + # When there are no PSI-BLAST hits generate an HMM from the query and run Jnet against that only. + # Accuracy won't be as good, but at least it's a prediction + if ( @seqs == 0 ) { + if ( $predNoHits == 0 ) { + warn "\nJPRED: Warning! no PSI-BLAST hits found and '-pred-nohits' option not set. Exiting...\n"; + print ">>100% complete\n"; + print $LOG "\nJPRED: Warning! no PSI-BLAST hits found and '-pred-nohits' option not set. Exiting...\n" if $LOG; + print $LOG ">>100% complete\n" if $LOG; + close($LOG) if $LOG; + exit; + } else { + print ">>50% complete\n"; + warn "\nJPRED: no PSI-BLAST hits found. Continuing with single query sequence only.\n\n"; + print "Running HMMer on query...\n" if $VERBOSE; + print $LOG ">>50% complete\n" if $LOG; + print $LOG "\nJPRED: no PSI-BLAST hits found. Continuing with single query sequence only.\n\n" if $LOG; + print $LOG "Running HMMer on query...\n" if $LOG; + + # copy input query to alignment + #system("cp $path $prefix.align") == 0 or croak "Error: unable to copy '$path'\n"; + open( my $ifh, "<", $infile ) or die "JPRED: cannot open file $infile: $!"; + open( my $ofh, ">", $prefix . ".align" ) or die "JPRED: cannot open file $prefix\.align: $!"; + while (<$ifh>) { print $ofh, $_ } + close $ifh; + close $ofh; + + # Temp files required for HMMer + my ( $hmmbuild_out, $hmmconvert_out ) = map { File::Temp->new->filename } 1 .. 2; + system("$hmmbuild -F --fast --amino --gapmax 1 --wblosum $hmmbuild_out $infile"); + system("$hmmconvert -F -p $hmmbuild_out $hmmconvert_out"); + unlink $hmmbuild_out; + + # Read in the HMMER file + my $hmmer = HMMER::Profile->new( read_file => $hmmconvert_out ); + + # Convert from HMMER::Profile to HMMER::Profile::Jnet + my $hmmer_jnet = HMMER::Profile::Jnet->new; + $hmmer_jnet->add_line( @{$_} ) for $hmmer->get_line; + $hmmer_jnet->write_file("$prefix.hmm"); + print ">>70% complete\n"; + print $LOG ">>70% complete\n" if $LOG; + + # Run Jnet for the prediction + print "Running JNet using the generated inputs from HMM only...\n" if $VERBOSE; + print $LOG "Running JNet using the generated inputs from HMM only...\n" if $LOG; + my $jnetlog = jnet( map { "$prefix.$_" } qw(hmm jnet) ); + print ">>90% complete\n"; + print $LOG ">>90% complete\n" if $LOG; + print $jnetlog if $VERBOSE; + print $LOG $jnetlog if $LOG; + } } else { + psiseq2fasta( "0.fasta.gz", @seqs ) if $DEBUG; + print ">>40% complete\n"; + print $LOG ">>40% complete\n" if $LOG; + + ##################################################################################################### + # Make PSIBLAST truncated alignments the right length + print "Untruncating the PSIBLAST alignments...\n" if $VERBOSE; + print $LOG "Untruncating the PSIBLAST alignments...\n" if $LOG; + @seqs = extend( $query, @seqs ); + psiseq2fasta( "1.fasta.gz", @seqs ) if $DEBUG; + + ##################################################################################################### + # Remove masking from PSIBLAST alignment + print "Unmasking the alignments...\n" if $VERBOSE; + print $LOG "Unmasking the alignments...\n" if $LOG; + my $idx = Index->new( type => "Index::FastaCMD" ) or die "Index type cannot be found."; + remove_seq_masks( $idx, $_ ) for @seqs[ 1 .. $#seqs ]; + psiseq2fasta( "2.fasta.gz", @seqs ) if $DEBUG; + + ##################################################################################################### + # Convert the sequences to upper case + print "Converting sequences to the same case...\n" if $VERBOSE; + print $LOG "Converting sequences to the same case...\n" if $LOG; + toupper($_) for @seqs; # CC sub is below + psiseq2fasta( "${prefix}_backup.fasta.gz", @seqs ); + + ##################################################################################################### + # Remove excessive sequences + print "Remove excessive sequences...\n" if $VERBOSE; + print $LOG "Remove excessive sequences...\n" if $LOG; + @seqs = reduce( $MAX_ALIGN, @seqs ); + psiseq2fasta( "3.fasta.gz", @seqs ) if $DEBUG; + + ##################################################################################################### + # Remove sequences that are too long or too short + print "Remove sequences which too long or short...\n" if $VERBOSE; + print $LOG "Remove sequences which too long or short...\n" if $LOG; + @seqs = del_long_seqs( 50, @seqs ); + psiseq2fasta( "4.fasta.gz", @seqs ) if $DEBUG; + + ##################################################################################################### + # Remove redundant sequences based upon pairwise identity and OC clustering + print "Remove redundant sequences...\n" if $VERBOSE; + print $LOG "Remove redundant sequences...\n" if $LOG; + @seqs = nonred( $NR_CUT, @seqs ); + psiseq2fasta( "5.fasta.gz", @seqs ) if $DEBUG; + + ##################################################################################################### + # Check that we haven't got rid of all of the sequences + if ( @seqs < 2 ) { + warn "JPRED: All the sequences found by PSIBLAST were removed during filtering, reverting to prefiltered sequences\n"; + print $LOG "JPRED: All the sequences found by PSIBLAST were removed during filtering, reverting to prefiltered sequences\n" if $LOG; + @seqs = fasta2psiseq("${prefix}_backup.fasta.gz"); + } + unlink("${prefix}_backup.fasta.gz") unless $DEBUG; + + # Remove gaps in the query sequence and same positions in the alignment + print "Removing gaps in the query sequence...\n" if $VERBOSE; + print $LOG "Removing gaps in the query sequence...\n" if $LOG; + degap(@seqs); + psiseq2fasta( "6.fasta.gz", @seqs ) if $DEBUG; + + # Output the alignment for the prediction + print "Outputting cleaned-up PSI_BLAST alignment...\n" if $VERBOSE; + print $LOG "Outputting cleaned-up PSI_BLAST alignment...\n" if $LOG; + psiseq2fasta( "$prefix.align", @seqs ); + + ##################################################################################################### + # Equivilent to getpssm script + print "Output the PSSM matrix from the PSI-BLAST profile...\n"; + print $LOG "Output the PSSM matrix from the PSI-BLAST profile...\n" if $LOG; + my $pssm = PSIBLAST::PSSM->new( read_file => "$prefix.profile" ); + $pssm->write_file("$prefix.pssm"); # CC write_file() sub is in Write.pm loaded via PSIBLAST::PSSM print ">>50% complete\n"; - warn "\nJPRED: no PSI-BLAST hits found. Continuing with single query sequence only.\n\n"; - print "Running HMMer on query...\n" if $VERBOSE; print $LOG ">>50% complete\n" if $LOG; - print $LOG "\nJPRED: no PSI-BLAST hits found. Continuing with single query sequence only.\n\n" if $LOG; - print $LOG "Running HMMer on query...\n" if $LOG; - - # copy input query to alignment - #system("cp $path $prefix.align") == 0 or croak "Error: unable to copy '$path'\n"; - open( my $ifh, "<", $infile ) or die "JPRED: cannot open file $infile: $!"; - open( my $ofh, ">", $prefix . ".align" ) or die "JPRED: cannot open file $prefix\.align: $!"; - while (<$ifh>) { print $ofh, $_ } - close $ifh; - close $ofh; - - # Temp files required for HMMer - my ( $hmmbuild_out, $hmmconvert_out ) = map { File::Temp->new->filename } 1 .. 2; - - system("$hmmbuild -F --fast --amino --gapmax 1 --wblosum $hmmbuild_out $infile"); - system("$hmmconvert -F -p $hmmbuild_out $hmmconvert_out"); - - # Read in the HMMER file - my $hmmer = HMMER::Profile->new( read_file => $hmmconvert_out ); - - # Convert from HMMER::Profile to HMMER::Profile::Jnet - my $hmmer_jnet = HMMER::Profile::Jnet->new; - $hmmer_jnet->add_line( @{$_} ) for $hmmer->get_line; - $hmmer_jnet->write_file("$prefix.hmm"); # write_file is in the Read.pm called from the HMMER::Profile module + + ##################################################################################################### + # Run HMMER on the sequences + print "Running HMMer on sequences found by PSI-BLAST...\n" if $VERBOSE; + print $LOG "Running HMMer on sequences found by PSI-BLAST...\n" if $LOG; + my $hmmer = hmmer(@seqs); # CC sub is below + $hmmer->write_file("$prefix.hmm"); # write_file is in the Read.pm called from the HMMER::Profile module print ">>70% complete\n"; print $LOG ">>70% complete\n" if $LOG; - +##################################################################################################### # Run Jnet for the prediction - print "Running JNet using the generated inputs from HMM only...\n" if $VERBOSE; - print $LOG "Running JNet using the generated inputs from HMM only...\n" if $LOG; - my $jnetlog = jnet( map { "$prefix.$_" } qw(hmm jnet) ); + print "Running JNet using the generated inputs from HMM and PSI-BLAST...\n" if $VERBOSE; + print $LOG "Running JNet using the generated inputs from HMM and PSI-BLAST...\n" if $LOG; + my $jnetlog = jnet( map { "$prefix.$_" } qw(hmm jnet pssm) ); # CC sub is below print ">>90% complete\n"; print $LOG ">>90% complete\n" if $LOG; - print $jnetlog if $VERBOSE; - print $LOG $jnetlog if $LOG; + print $jnetlog if $VERBOSE; + print $LOG $jnetlog if $LOG; } } else { - psiseq2fasta( "0.fasta.gz", @seqs ) if $DEBUG; - print ">>40% complete\n"; - print $LOG ">>40% complete\n" if $LOG; - - ##################################################################################################### - # Make PSIBLAST truncated alignments the right length - print "Untruncating the PSIBLAST alignments...\n" if $VERBOSE; - print $LOG "Untruncating the PSIBLAST alignments...\n" if $LOG; - @seqs = extend( $query, @seqs ); - psiseq2fasta( "1.fasta.gz", @seqs ) if $DEBUG; - - ##################################################################################################### - # Remove masking from PSIBLAST alignment - print "Unmasking the alignments...\n" if $VERBOSE; - print $LOG "Unmasking the alignments...\n" if $LOG; - my $idx = Index->new( type => "Index::FastaCMD" ) or die "Index type cannot be found."; - remove_seq_masks( $idx, $_ ) for @seqs[ 1 .. $#seqs ]; - psiseq2fasta( "2.fasta.gz", @seqs ) if $DEBUG; - - ##################################################################################################### - # Convert the sequences to upper case - print "Converting sequences to the same case...\n" if $VERBOSE; - print $LOG "Converting sequences to the same case...\n" if $LOG; - toupper($_) for @seqs; # CC sub is below - psiseq2fasta( "${prefix}_backup.fasta.gz", @seqs ); - - ##################################################################################################### - # Remove excessive sequences - print "Remove excessive sequences...\n" if $VERBOSE; - print $LOG "Remove excessive sequences...\n" if $LOG; - @seqs = reduce( $MAX_ALIGN, @seqs ); - psiseq2fasta( "3.fasta.gz", @seqs ) if $DEBUG; - - ##################################################################################################### - # Remove sequences that are too long or too short - print "Remove sequences which too long or short...\n" if $VERBOSE; - print $LOG "Remove sequences which too long or short...\n" if $LOG; - @seqs = del_long_seqs( 50, @seqs ); - psiseq2fasta( "4.fasta.gz", @seqs ) if $DEBUG; - - ##################################################################################################### - # Remove redundant sequences based upon pairwise identity and OC clustering - print "Remove redundant sequences...\n" if $VERBOSE; - print $LOG "Remove redundant sequences...\n" if $LOG; - @seqs = nonred( $NR_CUT, @seqs ); - psiseq2fasta( "5.fasta.gz", @seqs ) if $DEBUG; - - ##################################################################################################### - # Check that we haven't got rid of all of the sequences - if ( @seqs < 2 ) { - warn "JPRED: All the sequences found by PSIBLAST were removed during filtering, reverting to prefiltered sequences\n"; - print $LOG "JPRED: All the sequences found by PSIBLAST were removed during filtering, reverting to prefiltered sequences\n" if $LOG; - @seqs = fasta2psiseq("${prefix}_backup.fasta.gz"); + if ( 'fasta' eq $format ) { + print "Read FASTA file\n"; + my $hmmer1 = hmm_for_align($infile); + $hmmer1->write_file("$prefix.hmm"); # write_file is in the Read.pm called from the HMMER::Profile module + } elsif ( 'msf' eq $format ) { + msf2fasta( $infile, $infastafile ); + my $hmmer2 = hmm_for_align($infastafile); + $hmmer2->write_file("$prefix.hmm"); # write_file is in the Read.pm called from the HMMER::Profile module + } elsif ( 'blc' eq $format ) { + my $tmpfile = File::Temp->new->filename; + blc2msf( $infile, $tmpfile ); + msf2fasta( $infile, $infastafile ); + my $hmmer3 = hmm_for_align($infastafile); + $hmmer3->write_file("$prefix.hmm"); # write_file is in the Read.pm called from the HMMER::Profile module + } else { + die "ERROR! unknown input format '$format'. exit...\n"; } - unlink("${prefix}_backup.fasta.gz") unless $DEBUG; - - # Remove gaps in the query sequence and same positions in the alignment - print "Removing gaps in the query sequence...\n" if $VERBOSE; - print $LOG "Removing gaps in the query sequence...\n" if $LOG; - degap(@seqs); - psiseq2fasta( "6.fasta.gz", @seqs ) if $DEBUG; - - # Output the alignment for the prediction - print "Outputting cleaned-up PSI_BLAST alignment...\n" if $VERBOSE; - print $LOG "Outputting cleaned-up PSI_BLAST alignment...\n" if $LOG; - psiseq2fasta( "$prefix.align", @seqs ); - - ##################################################################################################### - # Equivilent to getpssm script - print "Output the PSSM matrix from the PSI-BLAST profile...\n"; - print $LOG "Output the PSSM matrix from the PSI-BLAST profile...\n" if $LOG; - my $pssm = PSIBLAST::PSSM->new( read_file => "$prefix.profile" ); - $pssm->write_file("$prefix.pssm"); # CC write_file() sub is in Write.pm loaded via PSIBLAST::PSSM - print ">>50% complete\n"; - print $LOG ">>50% complete\n" if $LOG; - - ##################################################################################################### - # Run HMMER on the sequences - print "Running HMMer on sequences found by PSI-BLAST...\n" if $VERBOSE; - print $LOG "Running HMMer on sequences found by PSI-BLAST...\n" if $LOG; - my $hmmer = hmmer(@seqs); # CC sub is below - $hmmer->write_file("$prefix.hmm"); # write_file is in the Read.pm called from the HMMER::Profile module print ">>70% complete\n"; print $LOG ">>70% complete\n" if $LOG; - - ##################################################################################################### +##################################################################################################### # Run Jnet for the prediction - print "Running JNet using the generated inputs from HMM and PSI-BLAST...\n" if $VERBOSE; - print $LOG "Running JNet using the generated inputs from HMM and PSI-BLAST...\n" if $LOG; - my $jnetlog = jnet( map { "$prefix.$_" } qw(hmm jnet pssm) ); # CC sub is below + print "Running JNet using the generated inputs from HMM only...\n" if $VERBOSE; + print $LOG "Running JNet using the generated inputs from HMM only...\n" if $LOG; + my $jnetlog = jnet( map { "$prefix.$_" } qw(hmm jnet) ); # CC sub is below print ">>90% complete\n"; print $LOG ">>90% complete\n" if $LOG; - print $jnetlog if $VERBOSE; - print $LOG $jnetlog if $LOG; + print $jnetlog if $VERBOSE; + print $LOG $jnetlog if $LOG; } unless ( defined $nofinal ) { my $aligfile = $prefix . ".align"; my $jnetfile = $prefix . ".jnet"; my $jnetfastafile = $prefix . ".jnet.fasta"; + $aligfile = $infile if ( 'fasta' eq $format ); + $aligfile = $infastafile if ( 'msf' eq $format or 'blc' eq $format ); concise2fasta( $jnetfile, $jnetfastafile ); open( my $IN1, "<", $aligfile ) or die "ERROR! unable to open '$aligfile': ${!}\nDied"; open( my $IN2, "<", $jnetfastafile ) or die "ERROR! unable to open '$jnetfastafile': ${!}\nDied"; @@ -538,22 +602,146 @@ unless ( defined $nofinal ) { close($IN2); close($OUT); unlink $jnetfastafile; + my $seqs = FASTA::File->new( read_file => $outfile ); + open( my $OUT2, ">", $outfile ) or die "ERROR! unable to open '$outfile': ${!}\n"; + $seqs->write($OUT2); + close($OUT2); } else { - if (defined $outfile and $prefix.".jnet" ne $outfile) { - rename $prefix.".jnet", $outfile; + if ( defined $outfile and $prefix . ".jnet" ne $outfile ) { + rename $prefix . ".jnet", $outfile; } } print ">>100% complete\n"; print "Jpred Finished\n"; print $LOG ">>100% complete\n" if $LOG; -print $LOG "Jpred Finished\n" if $LOG; -close ($LOG) if $LOG; +print $LOG "Jpred Finished\n" if $LOG; +close($LOG) if $LOG; exit; ##################################################################################################### # Functions ##################################################################################################### +sub check_FASTA_format { + my $infile = shift; + + open( my $IN, "<", $infile ) or die "ERROR! unable to open '$infile': ${!}\n"; + my $check_first_line = 1; + my $nseq = 0; + local $/ = "\n>"; + while (<$IN>) { + if ($check_first_line) { + return 0 unless (/^>/); + $check_first_line = 0; + } + s/^>//g; + s/>$//g; + + my ( $id, @seqs ) = split /\n/, $_; + return 0 unless ( defined $id or @seqs ); + my $seq = join( "", @seqs ); + return 0 unless ( $seq =~ /[a-zA-Z\.-]/ ); + ++$nseq; + } + close($IN); + + return $nseq; +} +##################################################################################################### +sub check_MSF_format { + my $infile = shift; + $? = 0; + system("$readseq -fMSF -a -p < $infile > /dev/null"); + return 0 if ($?); + + return 1; +} +##################################################################################################### +sub check_BLC_format { + my $infile = shift; + + my ( $tmpfile1, $tmpfile2 ) = map { File::Temp->new->filename } 1 .. 2; + open my $fh, ">$tmpfile1" or die "$tmpfile1: $!\n"; + print $fh "silent_mode\nblock_file $infile\n"; + print $fh "output_file /dev/null\nmax_nseq 2000\n"; + print $fh "pir_save $tmpfile2\nsetup\n"; + close $fh; + + $? = 0; + system("$alscript -s -f $tmpfile1"); + $? = 0; + system("$readseq -f8 -a -p < $tmpfile2 > /dev/null"); + unlink $tmpfile1; + unlink $tmpfile2; + return 0 if ($?); + + return 1; +} +############################################################################################################################################ +# convertor BLC -> MSF +sub msf2fasta { + my $infile = shift; + my $outfile = shift; + + my $sequence = ""; + open( my $IN, "<", $infile ) or die "ERROR! unable to open '$infile': ${!}\n"; + while (<$IN>) { + $sequence .= $_; + } + close($IN); + + $sequence =~ s/~/\./g; + + ## check for non-unique sequence names - readseq has problems with these + my @lines = split /\n/, $sequence; + my %names; + foreach my $line (@lines) { + if ( $line =~ /Name:\s+(\S+)/ ) { + die "ERROR! Alignment has non-unique sequence ids. exit...\n" if ( defined( $names{$1} ) && $names{$1} >= 1 ); + $names{$1}++; + } + } + + my $tmpfile1 = File::Temp->new->filename; + my $tmpfile2 = File::Temp->new->filename; + open my $FILE, ">$tmpfile1" or die "open $tmpfile1 failed: $!"; + print $FILE $sequence; + close $FILE; + + $? = 0; + system("$readseq -fMSF -a -p < $tmpfile1 > $tmpfile2"); + die "Reformatting of $infile failed. exit...\n" if ($?); + unlink $tmpfile1; + + $? = 0; + system("$readseq -f8 -a -p < $tmpfile2 > $outfile"); + die "Reformatting of $infile failed. exit...\n" if ($?); + unlink $tmpfile2; + + die "Reformatting the input alignment has failed. exit...\n" unless ( -e $outfile ); +} + +############################################################################################################################################ +# convertor BLC -> MSF +sub blc2msf { + my ( $in, $out ) = @_; + + my ( $tmp, $tmp_pir ) = map { File::Temp->new->filename } 1 .. 2; + + open my $fh, ">$tmp" or die "$tmp: $!\n"; + print $fh "silent_mode\nblock_file $infile\n"; + print $fh "output_file /dev/null\nmax_nseq 2000\n"; + print $fh "pir_save $tmp_pir\nsetup\n"; + close $fh; + + $? = 0; + system("$alscript -s -f $tmp"); + die "Reformatting of $infile failed. exit...\n" if ($?); + system("$readseq -f=MSF -o=$out -a $tmp_pir"); + + unlink $tmp; + unlink $tmp_pir; +} ##################################################################################################### @@ -959,6 +1147,41 @@ Runs Jnet. Pass the paths of the filenames to do the prediction on =cut +################################################################################################################################################# + +=head2 get_hmm($alignFile, $name) + +Adapted from the hmmer() function in Jpred as written by JDB. + +Generates an HMMer profile output compatible with Jnet. + +Equivilent to gethmm script. + +=cut + +sub hmm_for_align { + my $fastafile = shift; + + # Temp files required + print "hmm_for_align: fastafile = $fastafile\n"; + my ( $hmmbuild_out, $hmmconvert_out ) = map { File::Temp->new->filename } 1 .. 2; + + system("$hmmbuild -F --fast --amino --gapmax 1 --wblosum $hmmbuild_out $fastafile"); + system("$hmmconvert -F -p $hmmbuild_out $hmmconvert_out"); + + # Read in the HMMER file + my $hmmer = HMMER::Profile->new( read_file => $hmmconvert_out ); + + # Read in the HMMER file + my $hmmer_tmp = HMMER::Profile->new( read_file => $hmmconvert_out ); + + # Convert from HMMER::Profile to HMMER::Profile::Jnet + my $hmmer_jnet = HMMER::Profile::Jnet->new; + $hmmer_jnet->add_line( @{$_} ) for $hmmer_tmp->get_line; + + return $hmmer_jnet; +} + ##################################################################################################### sub jnet { my ( $hmmer, $outfile, $pssm ) = @_; @@ -972,7 +1195,7 @@ sub jnet { system("$jnet --concise --hmmer $hmmer > $outfile"); } check( "jnet", $? ) or exit 1; - my $res = ""; + my $res = ""; my $logging = ""; open( my $IN, "<", $outfile ) or die "ERROR! unable to open '$outfile': ${!}\nDied"; while (<$IN>) { @@ -984,7 +1207,7 @@ sub jnet { } close $IN; open( my $OUT, ">", $outfile ) or die "ERROR! unable to open '$outfile': ${!}\nDied"; - print $OUT "\n".$res; + print $OUT "\n" . $res; close $OUT; return $logging; } @@ -1097,6 +1320,8 @@ sub fasta2psiseq_lowmemory { return @seqs; } +##################################################################################################### + =head1 extend($FASTA::File, @PSISEQ) Sometimes PSIBLAST truncates the outputed alignment where it can't matched residues @@ -1105,7 +1330,6 @@ present in the alignment. The other sequences are extended with gap characters. =cut -##################################################################################################### sub extend { my ( $query, @seqs ) = @_; @@ -1156,13 +1380,14 @@ sub extend { return @seqs; } +##################################################################################################### + =head1 $int = fasta_seq_length($path) Given the path to a FASTA database, find the number of residues/bases in it. Counts whitespace as a residue. =cut -##################################################################################################### sub fasta_seq_length { my ($fn) = @_; open my $fh, $fn or croak "Can't open file $fn: $!\n"; @@ -1177,9 +1402,3 @@ sub fasta_seq_length { return $length; } - -=head1 log(@messages) - -Report messages to STDERR - -=cut diff --git a/binaries/src/jpred/lib/Paths.pm b/binaries/src/jpred/lib/Paths.pm index 9fa5ca3..9a51953 100644 --- a/binaries/src/jpred/lib/Paths.pm +++ b/binaries/src/jpred/lib/Paths.pm @@ -33,6 +33,8 @@ our @EXPORT_OK = qw( $hmmbuild $hmmconvert $psiblastbin + $alscript + $readseq check_OS setup_env ); @@ -58,6 +60,8 @@ our $fastacmd = "$SOFTDIR/$platform_name/fastacmd"; our $hmmbuild = "$SOFTDIR/$platform_name/hmmbuild"; our $hmmconvert = "$SOFTDIR/$platform_name/hmmconvert"; our $psiblastbin = "$SOFTDIR/$platform_name/blastpgp"; +our $alscript = "$SOFTDIR/$platform_name/alscript"; +our $readseq = "$SOFTDIR/$platform_name/readseq"; # required for training with SNNS, but unused currently our $ff_bignet = "$HOME/projects/Jnet/bin/snns/ff_bignet"; # CC modified for new path (SNNS app) @@ -87,6 +91,8 @@ sub setup_env { $hmmbuild = "$SOFTDIR/$platform_name/hmmbuild"; $psiblastbin = "$SOFTDIR/$platform_name/blastpgp"; $hmmconvert = "$SOFTDIR/$platform_name/hmmconvert"; + $alscript = "$SOFTDIR/$platform_name/alscript"; + $readseq = "$SOFTDIR/$platform_name/readseq"; } sub check_OS { @@ -103,8 +109,6 @@ sub check_OS { warn "check_OS: unknown platform, I'll try to use x86_64 binaries...."; } -# print "\n\ncheck_OS: SOFTDIR -> $SOFTDIR\n\n"; - $oc = "$SOFTDIR/$platform_name/oc"; $jnet = "$SOFTDIR/$platform_name/jnet"; $fastacmd = "$SOFTDIR/$platform_name/fastacmd"; @@ -112,6 +116,8 @@ sub check_OS { $hmmbuild = "$SOFTDIR/$platform_name/hmmbuild"; $psiblastbin = "$SOFTDIR/$platform_name/blastpgp"; $hmmconvert = "$SOFTDIR/$platform_name/hmmconvert"; + $alscript = "$SOFTDIR/$platform_name/alscript"; + $readseq = "$SOFTDIR/$platform_name/readseq"; return $platform_name; } diff --git a/binaries/src/jpred/tests/alignment.clustal b/binaries/src/jpred/tests/alignment.clustal new file mode 100644 index 0000000..509e0d8 --- /dev/null +++ b/binaries/src/jpred/tests/alignment.clustal @@ -0,0 +1,186 @@ +CLUSTAL W(1.60) multiple sequence alignment + +QUERY MKKIEAIIRPFKLDEVKIALVNAGIVGMTVSEVRGFGRQKGQTERYRGSEYTVEFLQKLK +UniRef90_C0EK60 MKKIEAIIKPFKLDDVREILTEIGITGMTVSEVKGFGRQKGHTEIYRGAEYAVDFLPKVK +UniRef90_Q21P81 MKLITAVIKPFKLDDVRNALSEIGVQGMTVTEVKGFGRQKGHTELYRGAEYVIDFLPKVK +UniRef90_Q47GI8 MKKIEAIIKPFKLDEVREALSEIGISGLTVTEVKGFGRQKGHTELYRGAEYVVDFLPKIK +UniRef90_B9ZJ79 MKKIEAIIKPFKLEDVREALTEMGIAGMTATEVQGFGRQKGHTELYRGAEYVVDFLPKVK +UniRef90_B5FAN6 MKIINAIIKPFKLDDVREALADAGVDGMTVSEVKGFGRQKGHTELYRGAEYQVDFLPKVK +UniRef90_B5ZIL8 MKKIEAIIKPFKLDEVKDALHEIGLMGISVTEAKGFGRQKGHTELYRGAEYIVDFLPKVK +UniRef90_B4RVM6 MKKIEAIIKPFKMDDVREALAEVGIAGMTVSEVKGFGRQKGHTELYRGAEYQVDFLPKIK +UniRef90_B2FHB8 MKLISAIIRPFKLDEVREALSDAGVSGITVTEVKGFGRQKGHTELYRGAEYVVDFLPKIK +UniRef90_P21193 MKKIEAIIKPFKLDEVKEALHEVGIKGITVTEAKGFGRQKGHTELYRGAEYVVDFLPKVK +UniRef90_B5JS45 MKKIEAVIKPFKLDDVRDALADIGVSGMTVTEVKGFGRQKGHTETYRGAEYVVDFLPKLK +UniRef90_Q07UM0 MKLVVAIIKPFKLDEVRQALTDVGVHGMTVTEVKGYGRQRGHTEIYRGAEYLVNFLPKLR +UniRef90_Q2RVB4 MKFVIAITKPFKLDEVREALGALGIQGMTVTEVKGFGRQKGQTEVYRGAEYVVNFLPKVK +UniRef90_A9IPV3 MKLIIAIIKPFKLDEVRVALSGIGVQGLTVTEVKGFGRQKGHTELYRGAEYAVDFLPKLR +UniRef90_A4TZT2 MKLIIAIIKPFKLDEVREALTQLGIQGLTATEVKGFGRQKGQTEIYRAAEYVVSFVPKIK +UniRef90_B3DVA4 --KIEAIIKPFKLEEVKEALTEIGIAGLTVTEVKGFGRQKGHTEIYRGSEYTVDFLPKVK +UniRef90_C1STD4 MRKIEIITRPFKLDEVKQRLTKLGIQGMTVTEVKGFGRQRGHKEIYRGAEYQVDFVAKVK +UniRef90_A7HGG9 MKRIEAIIRPSKLEDVRRLLSHPWISAMTVSEVRGAGRQKGHAELYRGAEYVIDLIPKLK +UniRef90_A9BCF1 MKKIEAIIRPFKLEDVKVALVNSGIVGMTVSEVRGFGRQKGQVERYRGSEFTVEFLQKLK +UniRef90_B4U911 MKKVEAIIKPFKLDEVKDALVEIGIGGMTITEVKGFGQQKGKTEIYRATEYVIDFLPKIK +UniRef90_B1ZSX2 MKLVTAIIKPFKLEEIKAALAEIQVEGMTVTEVKGFGRQKGHTEIYRGTEYTVDFLPKVR +UniRef90_Q7X1L4 MKKVEAIIKPFKLDAVKEAVTALGVYGMTVTEVKGYGQQKGHTEQYRGAEYVVEFITKIK +UniRef90_Q1NW36 MKKVEAIIKPFKLDAVKEAVTALGIHGMTVSEVKGFGRQKGHTEVYRGAEYVVDFVAKIK +UniRef90_C0GRX0 MKKLEIITRPFKVEAVKEALAGMGIKGMTLTDVKGFGRQMGHKEIYRGAEYDVDFLPKVK +UniRef90_B8DJ84 MKKIEAIIKPFKLDAVKDALIGIGVFGLTVTEVRGYGRQRGHVETYRGLEYEVQFNSKLK +UniRef90_Q6ARG9 MKKIEAIIKPFKLEEIKEALTELAITGMTISEVKGYGRQKGHKEMYRGAEYSIDFNPKLK +UniRef90_C1W154 MKLVTAIIQPHRLDAVKSALEAAGIRGMTVSEASGYGRQKGHTEVYRGAEYTIDLVPKIR +UniRef90_C1UII8 MKLVTAIVKPFKLDDVKNALELIGIAGLTVSEVQGFGRQRGHTEVYRGAEYQVDFVPKVR +UniRef90_UPI000 --KVTVITNQAKFYQLKTSLEAIGITGMTVIQVLGFGIQKGQPEYYRGNPIEATLLPKVK +UniRef90_C1T022 MKLVIAYIRPECLNAVKQELYAKKIYNMSVTNVLGSGRQKGFTETYRGVVMEVNLLKKLR +UniRef90_Q46G48 MKYIIAMIRPERLDAVKRELQKLEVNRLTVSSVAGYGAQKGHLEIYRATEHEANLLEKVK +UniRef90_A2RJQ2 MKKIEAIIRTDKLEDLKKALSDNGVHGMTVSQVLGYGEQKGFAEYVRGQRIETTLLSKIK +UniRef90_Q8KF33 MKKIEAIIRTSQYEAVKKALHEIDIDFFTWWDVTGQGNDKKHTEIYRGTVRDTSYISRRY +UniRef90_B1HTS9 MKKIEVIIRPEVFGAVRDGLAQQGIAGLSVSEIAGCGRQLGRTGLFRGNTYEIEFLPKLK +UniRef90_A2SPS9 MKMITAIIRPEKVDEVLNALEQNNIPGVTITEVLGRGEQGGVCLQYRAGKMQVKTLPKTK +UniRef90_C0EAH3 --KLVIVTRQSKFEELKAAMNAIEVTGMTVTQVIGCGTQKGATEFYRGVPVEMNLLPKIK +UniRef90_A7I8Z1 --MISAIIKPERFEFVKKALEDKGYVSMTITEVKGRGEQKGISLEYRGGKMTVDLLPKVK +UniRef90_Q3AFZ0 MKKIEALIRPQKLGEVKEALNKLGISGMTVTEVVGCGRQKGQKEIYRGIEYEINLLPKVK +UniRef90_A7I508 MKLVIALIRPERFGAVKKALEDKGYIGMTTAEAKGRGAQKGIALVYRGGRLTIDILVKVR +UniRef90_P51604 MKEIIAIIRPNKINRTKEVLDALGFSSMTANAVFGRGRQKAIVGELREEEGSMRYIPKRM +UniRef90_B0NXT3 --KINAIVREEKFEDVKEALNKIGVNGITVSQVMGCGAQKGFTEVIRGTKVDMMMRPKIK +UniRef90_A8YG01 ----------------KIALVNAGIVGMTVSEVRGFGRQKGQSERYRGSEYTVEFLQKLK +UniRef90_C0BMJ9 MKKVEAIIRKSKFDDVKKALHAIEVNFFSYWDVTGVGNEKQ-GHVYRGISYSTSDIQRRI +UniRef90_Q466Y2 MCKIEAIIKPMKLHEVKDALEEAGYPSLTVTDVKGRGQQKGIVQQWRGKKYCVDLLPKTK +UniRef90_O26760 MKEIVAIIRPEKLEEVKNALEAAGCHGMTVTEVRGRGRQLGITESYRGRDYRIDLLPKTK +UniRef90_A0LYN2 MKKIEAIIRKSEFDETKEALHSIGVTFFSYWDVTGVGNEKV-GHVYRGVSYSTADIQRRY +UniRef90_C1YA75 MKVVTAVIKPFKLDEVRAALLAFGVQGMTVSESSGYGRQRGHTEVYRGAEYTVELLPKVR +UniRef90_A8KX44 MKLVTAIVRPHRVDDVRAALTTYGVHGITVSQVTGFGLEMWRTQTYRGNAFHDESTSNIR +UniRef90_C0EZB6 --KLTIMCKEDRFAILKDAMSQIGVTGMTVSHVMGCGTQKGKTGQYRGVKIDMNLLPQLQ +UniRef90_Q11P32 MKKIEAIVKPSKLKAIQAGLIKIGIPCMTVVPVKGVGLQQGFPEIYRGTEKSIVLLSKVM +UniRef90_A7B6Y7 --KIEAIVREEKFEQVKSALQDIQVNGVTISQVMGYGTQRGYTEIVRGSEVDILLHPKIK +UniRef90_A7VSI5 --KVVILFNQDKFIELKDAMNAIGVTGMTVIHVMGCGVQKGNTRYYRGVKLDIVLLPKIK +UniRef90_A6G036 --KVEAMIRPFKLDDVKERLTELEVGGMTVTEVKGFGRTGGKTEFYRGSAYVIDFVPKIK +UniRef90_C0ES36 MIKVEAYVREDKFEDVKAALNAIGVNGLTVSQVMGCGIQRGYKEIVRGMQVDMQMQPKIK +UniRef90_B5IHX8 MKQIQAIVRPEKLDAVKDALVEIGINGITVTAVQGFGKQMGHTEVYRGVKVEAKLLTKMQ +UniRef90_B0MIE7 ---------PEKLTDVKHILEAHKVSGLMISNIMGYGNQKGFTQKYRGNELNSNLLPKIK +UniRef90_B4S395 MKLITAIIQEDKLDQVREALIQANISRISVSRISGHGRQE-DIDIYRGRKIAPNLRPKIK +UniRef90_P51254 MKKIEAIIRPFKLNEVKLALVKGGIGGMTVVKVSGFGRQKGQTERYKGSEYSIDIIDKIK +UniRef90_P71524 MKMIRAVVRPSKAEEVVDALAESGCVALTKMDVIGRGKQKG----IKIDQIYYDELPKTM +UniRef90_A8JI83 ---IEAIFRPWRLPFVIDTLSKYGIRGLTNTPVKGVGVQGGSRERYAGTEFGPNLVDKEK +UniRef90_B0CD03 MRTITAFIRPQQCDQVKLVLVQLGIIDITLSDVKGFGRQQGSLQQYRGSDAEIRLHRKLK +UniRef90_B1QY06 MKRIEAIIRPSKLEEIKEALKNNNINGVTISQVMGCGKQLGWKEYHRGTELITNVLPKIE +UniRef90_Q30VL0 MKLLIAYIRPEKLSTVKKALYARGIYAMSVTNALGSGQQKGFTETYRGIVTEVNLLKKVR +UniRef90_A0T2Q5 MKEVLAIIRPNMVSKTGKALEAVGFPAMTVIRCFGRGKEKGYIDAGEKLGMRMKYIPKRM +UniRef90_B3QXW9 MKEITAIIRINKMNETKKALIKAGISSFTASRVLGRGKGQVHYDLLKGAAEGYELVSKRY +UniRef90_B6YRQ4 MKKIEAIIRKTRFDEVKEALLEADIEWFSYSDVRGVGKARQ-ERIYRGVVYDTSSIERIQ +UniRef90_B0MJN0 MTKVDIIANQEKFEVLKHALSSIGITGMTVSHVMGCGMQKGSTEFYRGVPVDARLLPKMK +UniRef90_C2C1T3 --KIEIITRPNRFDVFQKALKEIGVSGLTVTKAVGTGLEKGMIELYRGTIKENNVHERMK +UniRef90_C1VTA2 --LVMAIVRPEKLSDVKAALAEAGAPSLTVTQVSGRGSQPAKTGQWRGEEYVIDLHQKIK +UniRef90_A3XNG5 MKKIEAIIRKSKFTAVKKALHDKGVNFFSYWDVTGLGNEKE-GHVYRGVSYSTSDIQRRY +UniRef90_P71525 MKEIIAIIRPSKMAQTKTVLEGLGFPAMTANRVLGRGKQKAIVGELGFEV-DMRYIPKTM +UniRef90_Q46C91 MKEIIAIIRPKKVVPTKEALEKLGVPSLTAIPVFGRGKQKGIATELDIAGRRMEYIPKRL +UniRef90_B7BWA8 MKEVMIILRPKMYFPTKDALDQAGFHSMTIREIIGRGKCPVHYDYDEGAPVKHRLVAKRM +UniRef90_Q7UGU6 MKLIIAIVQPSKLDAIKEALTRVEVHRLTVVDCQGFGRQRGQTGSMRGRDYGVSLLRKVQ +UniRef90_A3HVG6 MKKIEAIIRTSRFEQIHSCVAGLGVKFLTFYEVKGMGLEHAKQQTYRGVAYEPTYIPRTK +UniRef90_A0YMH7 MKRIEALIRPVQFDSVVTALVEAGIVGMSVTNVRGYGRQKGQTESYRGVKHVIEFHPKMK +UniRef90_Q46A23 MKYIIAMIRPEKLDSVKKEIQKIGAHGLTVSSISGYGAQGGHLNVDRTKKYEANLLDKVK +UniRef90_B4VJP7 ----------------MKALLDAGYPAVTKVDVFGRGKQRG----LKIGNVLYDELPKAL +UniRef90_B1QUW3 MYLVRAIIRTEKVNGVLSELVDAGFPQVTKMDVFGRGKQKG----IQVGEVHYDELPKEM +UniRef90_A5N1U1 MKEIMAVIRMNMVGKTKKALAENGFPSITCKDVLGRGKKMVEEELHRIEDESYRLISKRL +UniRef90_A9D1T1 -----------------------------------------------GAEYMVDFLPKVK +UniRef90_A6LUZ0 MYMIRAIIRPERVSTVLSELLDAGFPEVTKMAVYGRGKQKG----IKVGEVYYDELPKEM +UniRef90_A6LUZ1 MKEVMCIIRLNKVNKTKEALAEAGFPSITCRKVLGRGKKSALVEAYMETGEVPRLIPKRF +UniRef90_B8GEW5 MKEIMAIVRMKKTGVTKRALVETGVAGFTALKVLGRGKLVEDTAVIEPAEQEVRFFPRRL +UniRef90_C1FI34 --QVRAMVRPWRLSGVIDALNKYGIRGLTTYTVHGAGVQIGTVERYAGSTFDANLVEKVV +UniRef90_C1TA34 MKEIIAIIRMNKVNITKKALADVGVCGLHAIKVMGRGKQLGVREEIDGLSGGTRLIPKRL +UniRef90_C1T440 MKEVIAVIRMNMMNKTKKALQDAGVVAFFAHEAFGRGKGLVDVKPLEGARKGIELYPKRM +UniRef90_A9A2H4 MKKVEAIVNESAQNAVIDAMRKVGISGVTVSKVQGQGAQD--------PPLVGDFFSRVL +UniRef90_Q97ME3 MKEIMAIIRMNMVEKTKEALLKGGNPAITCLKVLGRGRQKVDIEDYKMAEELSELISKRL + +QUERY LEIVVEDAQVDTVIDKIVAAARTGENGDGKIFVSPVDQTIRIRTGEKNADAISAWS +UniRef90_C0EK60 IELVLADDKVDQAVDAILETAHSGKIGDGKIFIYPVEEAIRIRTGERSEAAL---- +UniRef90_Q21P81 LELVLGDELIDQAVEAISKAAQTGKIGDGKIFITPCEEVIRIRTGETGPEAV---- +UniRef90_Q47GI8 IEIVVNSNNVEPAIDAIIKAARTGKIGDGKIFVMPVEQVVRIRTGETDEAAV---- +UniRef90_B9ZJ79 LELVVDDDRVDACIDAIVKASRTGKIGDGKIFVSDMARVVRIRTGEEGSEAL---- +UniRef90_B5FAN6 LEIAVQAEGVDRIVEAISKAAHTGKIGDGKIFVYDLQQAVRIRTGETDTEAL---- +UniRef90_B5ZIL8 LEIVCADNLVDRAVETIMAAARTGRIGDGKIFILPVEDVIRIRTGEHGEEAI---- +UniRef90_B4RVM6 IELVLDDDRVEQAVEAIQSSAKTGKIGDGKIFVYSVESAVRIRTGEQNEDAI---- +UniRef90_B2FHB8 IETVVTDERADAVIEAIQSSAGTGKIGDGKIFVTAVEQVIRIRTGEIGADAL---- +UniRef90_P21193 IEVVMEDSLVERAIEAIQQAAHTGRIGDGKIFVTPVEEVVRIRTGEKGGDAI---- +UniRef90_B5JS45 LEIVVAEKDADACVESITNAAKTGQIGDGKIFVSDVERTIRIRTGEEDESAI---- +UniRef90_Q07UM0 IEVGVADTLVDKAVEAITRSARTGQIGDGKIFVTPLDHALRIRTGETNADAL---- +UniRef90_Q2RVB4 IELAVPDNLLDQVVETIQSTAQTGKIGDGKIFVFDLGEAVRIRTGERGEEAL---- +UniRef90_A9IPV3 VEAAVPDHLVDQVIDVIEQAARTGKIGDGKIFTAPLEQVIRIRTGESGEAAL---- +UniRef90_A4TZT2 IELVVNDDVVDRAVEAIQAAARTDKIGDGKIFVMDVAHALRIRTGEADTEAL---- +UniRef90_B3DVA4 VEIVLTEDILPKAVEAIIKSAKTGKIGDGKIFVLPVSEAIRIRTEEKGENAI---- +UniRef90_C1STD4 IEIVVDDGLVEEIVSTVQEGARTGKVGDGKIFISPVDNAVRIRTGESGAEAL---- +UniRef90_A7HGG9 LEIVLPDPLVDRVVADLESWLRTGRIGDGKIFVEPLDDAVRVRTGERGEDAL---- +UniRef90_A9BCF1 IEIVVADESVPTVLTAIAEAAKTGEIGDGKIFISPVESVVRIRTGELDGSAL---- +UniRef90_B4U911 IETVVKDSEVEKVVQTILKSAQTGKVGDGKIFIYNVEETVRIRTGERGESAI---- +UniRef90_B1ZSX2 IEILAADESVPKILETIISTAKTGKIGDGKIFISAAEDVVRIRTDERGEAAL---- +UniRef90_Q7X1L4 VEIVVADAKVSPVLEAIRRTAMSNSIGDGKVFVSPVETALRIRTGETGDAAL---- +UniRef90_Q1NW36 VEIVVESEKASLLVETITQAARNGNIGDGKIFVTPVESVCRIRTGELDQDAI---- +UniRef90_C0GRX0 IEVILDDANVDQAVEAAIKAARTDKVGDGKIFVYSVENAIRIRTGESGDEAI---- +UniRef90_B8DJ84 IETVVPDGMSDQVVKAITTAARTGSIGDGKIFISSLEEVIRIRTGEEGTDAI---- +UniRef90_Q6ARG9 IELVVRAEIADKVVEKIRLAARTGKIGDGKIFVLPIEEVVRVRTGEQGREAI---- +UniRef90_C1W154 LEILVDDPDAHRVGEVITQAAHTGRIGDGKVWTIPVDSVTRVRTGEEGPSAL---- +UniRef90_C1UII8 IEVVVGEIEAARVVDAIVEAASTGQIGDGKVWVTTIDEIVRVRTGERGADAL---- +UniRef90_UPI000 MKKIEAIIRPEAFQTLKDGLSAVGISGLTVTEAAGCGKQQGKKGVFRGTSFEIQLVPRVK +UniRef90_C1T022 LEIGVNDDFAEQAVEAINAGARTGKEGDGVIFVLECAAAVRIRTQETGPAAMG--- +UniRef90_Q46G48 IEIAVEDHFLKSVIEAIKTGAKDGYIGSGKIFVLPLENVIRIRTNETGPEAL---- +UniRef90_A2RJQ2 IEIVSIDEKVDQIVNVITKAVRTGEVGDGKIFIQPVERVIRIRTSEEDAQAL---- +UniRef90_Q8KF33 LSIVVRDVNLQKTVDCLIKNARTGEVGDGKIFVSDIEQSYRIRTGESGDESL---- +UniRef90_B1HTS9 LEMIVDDSKVDGIVEILLREAATGKVGDGKIFIYPVEQAIRIRTKEVGSIAV---- +UniRef90_A2SPS9 LEIVVPDKDVDTLIKVIREHARTGKKGDGRIFVLPVEAAAWVRTDE---------- +UniRef90_C0EAH3 VEIVVCRVPVRTVIETAKKVLYTGHYGDGKIFVYDIENVVKVRTGEEGCAALQ--- +UniRef90_A7I8Z1 IEIVIRDKDLEDVIATLTGAARTGKIGDGKIFVIPVEKSIRIRTGD---------- +UniRef90_Q3AFZ0 IEIVTVDEKVEEIIKIISESARTGAIGDGKIFISEVLDAVRIRTGERGTAAITS-- +UniRef90_A7I508 IEIVSHDRDVEDLVSTIRESAWTGANGDGRIFVLPVEQAIRIRTGE---------- +UniRef90_P51604 ISLVVPDEDASLVVESIMKVNKTGQIGDGKIFVCPIEDAVRVRTKESGEDAI---- +UniRef90_B0NXT3 FEIVVSSEEWERTIEAIQKSAFTGEVGDGKIFSYEVRNVVKIRTGERDVDALQD-- +UniRef90_A8YG01 IEIVVEDKQVDMVVDKLISAARTGEIGDGKIFISPVEQIVRIRTGEKDLQAI---- +UniRef90_C0BMJ9 LSIVISDEFLEPTINAILEAACTGNVGDGKIFVSDVQDAYRIRTRENGKAGIN--- +UniRef90_Q466Y2 IEIAAPEDKIEEIIKIIQSSAYTGEIGDGKIFVTPIETVVRIRTGERNGDAL---- +UniRef90_O26760 IEIVVNDEDVDTVVETIVKSAQTGDIGDGKIFISGVDEVVRIRTGESGKKAV---- +UniRef90_A0LYN2 LSIVVTDSFVEKTVETLLKAAHTGKVGDGKIFILPVEEAYRIRTKEKGGESL---- +UniRef90_C1YA75 VEILVDDEDAEDVVDVIVRAARTGKIGDGKVWTQPVETVIRVRTGERGPEAL---- +UniRef90_A8KX44 LELVVADSDAPDVVNVIRRTAASTSSGAGKIWVLPVEGLARIRTGERGADAL---- +UniRef90_C0EZB6 VDIVVSTVPPELVVEAAKKALYTGEYGDGKIFLYDVENVVRIRTNETGIAAL---- +UniRef90_Q11P32 IICVVSDENLEKCIDVIIETGSEGKVGDGKIFVYDVLDAIRMRTRTRGDDAI---- +UniRef90_A7B6Y7 FEVVVSSEEWEQTISAIQKAAFTGEVGDGKIFSYEIRSAVKIRTKETGYNAVQS-- +UniRef90_A7VSI5 LEIVVSKVPVQTV-DTARKVLYTGNIGDGKIFIYDVENVIKVRTGAEGYYALQD-- +UniRef90_A6G036 IEVVVPAARSEEVIAAIREVAASDRIGDGKIFVTPVLEAVRIRTDERGESAL---- +UniRef90_C0ES36 FEIVVSSEEWEKTIEAIEKAAYTGEPGDGKIFTYEIRHAQKIRTKETGYDAIQAT- +UniRef90_B5IHX8 ITSVVTDQAVDQVVQAILTAARTGEIGDGKIVITPVENAIRIRTGESGDSTLA--- +UniRef90_B0MIE7 VESVMPEEVVEKVTKDIVNTVRTGEFGDGKIFISPVEEAIRIRTGETGKDAL---- +UniRef90_B4S395 LEIAVNEEFVDVAIDTIVDSARSGEIGDGKIFVTPLEQCVRIRTNERGGSAI---- +UniRef90_P51254 IEIIVSDDKVNSITEIIIKTAKTGEIGDGKIFISDVEQVIRIRTNDLNSAAL---- +UniRef90_P71524 LMLVVEDDAAENVIELITKTAYTGSFGDGKIFVSPVDEAYTVRTRSCG-------- +UniRef90_A8JI83 LDIVVSRAQVDAVVRLVAASAYTGEIGDGKIFVHPVAEVVRIRTAETG-------- +UniRef90_B0CD03 VEVKVDEEMVAPVVEKITFAARTGQVGDGKIFVSPLQKVVQVRTGEE--------- +UniRef90_B1QY06 VKMVIEDSKVEEVIEIISSIAKTGEVGDGKIFVIDICDCVRIRTGERGNEAL---- +UniRef90_Q30VL0 IEVGVPADKAEDALAALQTGAHTGREGDGIIFVQDVARTVRVRTGE---------- +UniRef90_A0T2Q5 ISIVVDDADVPFVVGIIMKVNRTGKPGDGKIFVLPVEEAIRIRTGEFGVEAIG--- +UniRef90_B3QXW9 LVVVVNDNMLQPTIDAIISANQTGKPGDGKIFVSTIEDAVRVRTGETGSAIL---- +UniRef90_B6YRQ4 INLVVRDINVEKAIKAIEKSAHTGEVGDGRIFVSTIDNAYSIRTGEQGDETL---- +UniRef90_B0MJN0 VEIVVCKVPVEKVVEVAKNALYTGKIGDGKIFVYDVENVIKVRTGEEAYEALQD-- +UniRef90_C2C1T3 VEIVVSTVPVEAVLEVVKNTLRTGEPGDGKVFVYPLSDVIKISTGEHGVAALQD-- +UniRef90_C1VTA2 VECVVEPEDADDVVEAIREGANTGEKGDGKIFVLPVFDAVQVRTGDRGTDAI---- +UniRef90_A3XNG5 LSIVVNDDFEQAAVAAILDAAATGEVGDGKIFVSDVQDAYRIRTGKKGPDTLN--- +UniRef90_P71525 LTLIVPDEDASLVVEAIMKVNKSGQYGDGKIFVCPIEDIITVRTSERGEAAI---- +UniRef90_Q46C91 FSIVTRNEDVDTIIETIMKVNQTGDIGDGRIFICPVDDAIRVRTDEHGDNAL---- +UniRef90_B7BWA8 IDMFVRDEDLQKLIDTVVEVNKTNHAGDGKIFVLPVNDAIRVRTGEKGIEAI---- +UniRef90_Q7UGU6 LQIGVNEEFVQPTIDAIGRSGESGEIGDGKIFVLPMDDCVRIRTGERGGEAI---- +UniRef90_A3HVG6 LEIVTVDELVEPVINCILTEGKTGEVGDGKIFVYDVLEAHRIRNNDQGEQAL---- +UniRef90_A0YMH7 LEIVVEDEVCEFVVEKLVEAAQTGQIGDGKIFIQSMEHIIRTRTGESDLEAL---- +UniRef90_Q46A23 IEIAVKDEFLQTTVEAIERGSKDGYIGSGKIFVLPLENVMRIRTKETGNDAL---- +UniRef90_B4VJP7 LMVVVPDTEKEFVIRAILSSARTGAEGDGKIFVSPVEEVYTISSGKTDSS------ +UniRef90_B1QUW3 LLIVVKDEDKDDVVRVIMKNSRTGEYGDGKIFISKVDTAYTISTGKE--------- +UniRef90_A5N1U1 IWILAKDEDVKKIADIIIDINQTGHPGDGKIFVTKVTDVVRIRTGETQDEAV---- +UniRef90_A9D1T1 IELVIQDELLDRAIEVIVDTARTGKIGDGKIFVTEIERVIRIRTGEENEEAV---- +UniRef90_A6LUZ0 LLIAVKDEDKDDVIKVIIRNSRTGEFGDGKIFVAPIEEVYTVSSGKSG-------- +UniRef90_A6LUZ1 ITLVVKDDEVKTVVDTVISVNSTGTPGDGKIFVLPVEEVYRVRDGQIGEEAI---- +UniRef90_B8GEW5 FTILAHDEDVPRIVEAITKVNITEKVGDGIILVLPVDDAVRVRTGESGDAAI---- +UniRef90_C1FI34 VEIVVVREQCQEVVDVIVDAAQTGEIGDGKIFLSPVHDIVRIRTGEVGAAA----- +UniRef90_C1TA34 LTILARDEDVKKIVDTVIKVNQEGNKGDGRIFIAPVIDAYRVRTAEKGEAAV---- +UniRef90_C1T440 LTVVVTDDLVPEVVKVITDTNKTGQPGDGKIFVLPMIDAVRVRTGEKGAKSI---- +UniRef90_A9A2H4 IVCVVDDPKLDEILDAIAGAACTGTKGDGKVYVSDICDALDICTKKRG-------- +UniRef90_Q97ME3 IIILAKDEDVKEIVDEIIEVNRTGNPGDGKIFVINIADAMRIRTEETGDMAI---- + +QUERY UniRef90_C0EK60 UniRef90_Q21P81 UniRef90_Q47GI8 UniRef90_B9ZJ79 UniRef90_B5FAN6 UniRef90_B5ZIL8 UniRef90_B4RVM6 UniRef90_B2FHB8 UniRef90_P21193 UniRef90_B5JS45 UniRef90_Q07UM0 UniRef90_Q2RVB4 UniRef90_A9IPV3 UniRef90_A4TZT2 UniRef90_B3DVA4 UniRef90_C1STD4 UniRef90_A7HGG9 UniRef90_A9BCF1 UniRef90_B4U911 UniRef90_B1ZSX2 UniRef90_Q7X1L4 UniRef90_Q1NW36 UniRef90_C0GRX0 UniRef90_B8DJ84 UniRef90_Q6ARG9 UniRef90_C1W154 UniRef90_C1UII8 UniRef90_UPI000 IEIVVCKIPTETVVATIKTALYTGHIGDGKIFVHAVENVHRISTGEEGYDALQD--VEMV +UniRef90_C1T022 UniRef90_Q46G48 UniRef90_A2RJQ2 UniRef90_Q8KF33 UniRef90_B1HTS9 UniRef90_A2SPS9 UniRef90_C0EAH3 UniRef90_A7I8Z1 UniRef90_Q3AFZ0 UniRef90_A7I508 UniRef90_P51604 UniRef90_B0NXT3 UniRef90_A8YG01 UniRef90_C0BMJ9 UniRef90_Q466Y2 UniRef90_O26760 UniRef90_A0LYN2 UniRef90_C1YA75 UniRef90_A8KX44 UniRef90_C0EZB6 UniRef90_Q11P32 UniRef90_A7B6Y7 UniRef90_A7VSI5 UniRef90_A6G036 UniRef90_C0ES36 UniRef90_B5IHX8 UniRef90_B0MIE7 UniRef90_B4S395 UniRef90_P51254 UniRef90_P71524 UniRef90_A8JI83 UniRef90_B0CD03 UniRef90_B1QY06 UniRef90_Q30VL0 UniRef90_A0T2Q5 UniRef90_B3QXW9 UniRef90_B6YRQ4 UniRef90_B0MJN0 UniRef90_C2C1T3 UniRef90_C1VTA2 UniRef90_A3XNG5 UniRef90_P71525 UniRef90_Q46C91 UniRef90_B7BWA8 UniRef90_Q7UGU6 UniRef90_A3HVG6 UniRef90_A0YMH7 UniRef90_Q46A23 UniRef90_B4VJP7 UniRef90_B1QUW3 UniRef90_A5N1U1 UniRef90_A9D1T1 UniRef90_A6LUZ0 UniRef90_A6LUZ1 UniRef90_B8GEW5 UniRef90_C1FI34 UniRef90_C1TA34 UniRef90_C1T440 UniRef90_A9A2H4 UniRef90_Q97ME3 +QUERY UniRef90_C0EK60 UniRef90_Q21P81 UniRef90_Q47GI8 UniRef90_B9ZJ79 UniRef90_B5FAN6 UniRef90_B5ZIL8 UniRef90_B4RVM6 UniRef90_B2FHB8 UniRef90_P21193 UniRef90_B5JS45 UniRef90_Q07UM0 UniRef90_Q2RVB4 UniRef90_A9IPV3 UniRef90_A4TZT2 UniRef90_B3DVA4 UniRef90_C1STD4 UniRef90_A7HGG9 UniRef90_A9BCF1 UniRef90_B4U911 UniRef90_B1ZSX2 UniRef90_Q7X1L4 UniRef90_Q1NW36 UniRef90_C0GRX0 UniRef90_B8DJ84 UniRef90_Q6ARG9 UniRef90_C1W154 UniRef90_C1UII8 UniRef90_UPI000 IEESRLDEIVDVIIDSCSTDTIGDGK-------------------------- +UniRef90_C1T022 UniRef90_Q46G48 UniRef90_A2RJQ2 UniRef90_Q8KF33 UniRef90_B1HTS9 UniRef90_A2SPS9 UniRef90_C0EAH3 UniRef90_A7I8Z1 UniRef90_Q3AFZ0 UniRef90_A7I508 UniRef90_P51604 UniRef90_B0NXT3 UniRef90_A8YG01 UniRef90_C0BMJ9 UniRef90_Q466Y2 UniRef90_O26760 UniRef90_A0LYN2 UniRef90_C1YA75 UniRef90_A8KX44 UniRef90_C0EZB6 UniRef90_Q11P32 UniRef90_A7B6Y7 UniRef90_A7VSI5 UniRef90_A6G036 UniRef90_C0ES36 UniRef90_B5IHX8 UniRef90_B0MIE7 UniRef90_B4S395 UniRef90_P51254 UniRef90_P71524 UniRef90_A8JI83 UniRef90_B0CD03 UniRef90_B1QY06 UniRef90_Q30VL0 UniRef90_A0T2Q5 UniRef90_B3QXW9 UniRef90_B6YRQ4 UniRef90_B0MJN0 UniRef90_C2C1T3 UniRef90_C1VTA2 UniRef90_A3XNG5 UniRef90_P71525 UniRef90_Q46C91 UniRef90_B7BWA8 UniRef90_Q7UGU6 UniRef90_A3HVG6 UniRef90_A0YMH7 UniRef90_Q46A23 UniRef90_B4VJP7 UniRef90_B1QUW3 UniRef90_A5N1U1 UniRef90_A9D1T1 UniRef90_A6LUZ0 UniRef90_A6LUZ1 UniRef90_B8GEW5 UniRef90_C1FI34 UniRef90_C1TA34 UniRef90_C1T440 UniRef90_A9A2H4 UniRef90_Q97ME3 diff --git a/binaries/src/jpred/tests/alignment.fasta b/binaries/src/jpred/tests/alignment.fasta new file mode 100644 index 0000000..aa2b047 --- /dev/null +++ b/binaries/src/jpred/tests/alignment.fasta @@ -0,0 +1,267 @@ +>QUERY/1-116 +MKKIEAIIRPFKLDEVKIALVNAGIVGMTVSEVRGFGRQKGQTERYRGSEYTVEFLQKLK +LEIVVEDAQVDTVIDKIVAAARTGENGDGKIFVSPVDQTIRIRTGEKNADAISAWS +>UniRef90_C0EK60/1-112 +MKKIEAIIKPFKLDDVREILTEIGITGMTVSEVKGFGRQKGHTEIYRGAEYAVDFLPKVK +IELVLADDKVDQAVDAILETAHSGKIGDGKIFIYPVEEAIRIRTGERSEAAL---- +>UniRef90_Q21P81/1-112 +MKLITAVIKPFKLDDVRNALSEIGVQGMTVTEVKGFGRQKGHTELYRGAEYVIDFLPKVK +LELVLGDELIDQAVEAISKAAQTGKIGDGKIFITPCEEVIRIRTGETGPEAV---- +>UniRef90_Q47GI8/1-112 +MKKIEAIIKPFKLDEVREALSEIGISGLTVTEVKGFGRQKGHTELYRGAEYVVDFLPKIK +IEIVVNSNNVEPAIDAIIKAARTGKIGDGKIFVMPVEQVVRIRTGETDEAAV---- +>UniRef90_B9ZJ79/1-112 +MKKIEAIIKPFKLEDVREALTEMGIAGMTATEVQGFGRQKGHTELYRGAEYVVDFLPKVK +LELVVDDDRVDACIDAIVKASRTGKIGDGKIFVSDMARVVRIRTGEEGSEAL---- +>UniRef90_B5FAN6/1-112 +MKIINAIIKPFKLDDVREALADAGVDGMTVSEVKGFGRQKGHTELYRGAEYQVDFLPKVK +LEIAVQAEGVDRIVEAISKAAHTGKIGDGKIFVYDLQQAVRIRTGETDTEAL---- +>UniRef90_B5ZIL8/1-112 +MKKIEAIIKPFKLDEVKDALHEIGLMGISVTEAKGFGRQKGHTELYRGAEYIVDFLPKVK +LEIVCADNLVDRAVETIMAAARTGRIGDGKIFILPVEDVIRIRTGEHGEEAI---- +>UniRef90_B4RVM6/1-112 +MKKIEAIIKPFKMDDVREALAEVGIAGMTVSEVKGFGRQKGHTELYRGAEYQVDFLPKIK +IELVLDDDRVEQAVEAIQSSAKTGKIGDGKIFVYSVESAVRIRTGEQNEDAI---- +>UniRef90_B2FHB8/1-112 +MKLISAIIRPFKLDEVREALSDAGVSGITVTEVKGFGRQKGHTELYRGAEYVVDFLPKIK +IETVVTDERADAVIEAIQSSAGTGKIGDGKIFVTAVEQVIRIRTGEIGADAL---- +>UniRef90_P21193/1-112 +MKKIEAIIKPFKLDEVKEALHEVGIKGITVTEAKGFGRQKGHTELYRGAEYVVDFLPKVK +IEVVMEDSLVERAIEAIQQAAHTGRIGDGKIFVTPVEEVVRIRTGEKGGDAI---- +>UniRef90_B5JS45/1-112 +MKKIEAVIKPFKLDDVRDALADIGVSGMTVTEVKGFGRQKGHTETYRGAEYVVDFLPKLK +LEIVVAEKDADACVESITNAAKTGQIGDGKIFVSDVERTIRIRTGEEDESAI---- +>UniRef90_Q07UM0/1-112 +MKLVVAIIKPFKLDEVRQALTDVGVHGMTVTEVKGYGRQRGHTEIYRGAEYLVNFLPKLR +IEVGVADTLVDKAVEAITRSARTGQIGDGKIFVTPLDHALRIRTGETNADAL---- +>UniRef90_Q2RVB4/1-112 +MKFVIAITKPFKLDEVREALGALGIQGMTVTEVKGFGRQKGQTEVYRGAEYVVNFLPKVK +IELAVPDNLLDQVVETIQSTAQTGKIGDGKIFVFDLGEAVRIRTGERGEEAL---- +>UniRef90_A9IPV3/1-112 +MKLIIAIIKPFKLDEVRVALSGIGVQGLTVTEVKGFGRQKGHTELYRGAEYAVDFLPKLR +VEAAVPDHLVDQVIDVIEQAARTGKIGDGKIFTAPLEQVIRIRTGESGEAAL---- +>UniRef90_A4TZT2/1-112 +MKLIIAIIKPFKLDEVREALTQLGIQGLTATEVKGFGRQKGQTEIYRAAEYVVSFVPKIK +IELVVNDDVVDRAVEAIQAAARTDKIGDGKIFVMDVAHALRIRTGEADTEAL---- +>UniRef90_B3DVA4/1-110 +--KIEAIIKPFKLEEVKEALTEIGIAGLTVTEVKGFGRQKGHTEIYRGSEYTVDFLPKVK +VEIVLTEDILPKAVEAIIKSAKTGKIGDGKIFVLPVSEAIRIRTEEKGENAI---- +>UniRef90_C1STD4/1-112 +MRKIEIITRPFKLDEVKQRLTKLGIQGMTVTEVKGFGRQRGHKEIYRGAEYQVDFVAKVK +IEIVVDDGLVEEIVSTVQEGARTGKVGDGKIFISPVDNAVRIRTGESGAEAL---- +>UniRef90_A7HGG9/1-112 +MKRIEAIIRPSKLEDVRRLLSHPWISAMTVSEVRGAGRQKGHAELYRGAEYVIDLIPKLK +LEIVLPDPLVDRVVADLESWLRTGRIGDGKIFVEPLDDAVRVRTGERGEDAL---- +>UniRef90_A9BCF1/1-112 +MKKIEAIIRPFKLEDVKVALVNSGIVGMTVSEVRGFGRQKGQVERYRGSEFTVEFLQKLK +IEIVVADESVPTVLTAIAEAAKTGEIGDGKIFISPVESVVRIRTGELDGSAL---- +>UniRef90_B4U911/1-112 +MKKVEAIIKPFKLDEVKDALVEIGIGGMTITEVKGFGQQKGKTEIYRATEYVIDFLPKIK +IETVVKDSEVEKVVQTILKSAQTGKVGDGKIFIYNVEETVRIRTGERGESAI---- +>UniRef90_B1ZSX2/1-112 +MKLVTAIIKPFKLEEIKAALAEIQVEGMTVTEVKGFGRQKGHTEIYRGTEYTVDFLPKVR +IEILAADESVPKILETIISTAKTGKIGDGKIFISAAEDVVRIRTDERGEAAL---- +>UniRef90_Q7X1L4/1-112 +MKKVEAIIKPFKLDAVKEAVTALGVYGMTVTEVKGYGQQKGHTEQYRGAEYVVEFITKIK +VEIVVADAKVSPVLEAIRRTAMSNSIGDGKVFVSPVETALRIRTGETGDAAL---- +>UniRef90_Q1NW36/1-112 +MKKVEAIIKPFKLDAVKEAVTALGIHGMTVSEVKGFGRQKGHTEVYRGAEYVVDFVAKIK +VEIVVESEKASLLVETITQAARNGNIGDGKIFVTPVESVCRIRTGELDQDAI---- +>UniRef90_C0GRX0/1-112 +MKKLEIITRPFKVEAVKEALAGMGIKGMTLTDVKGFGRQMGHKEIYRGAEYDVDFLPKVK +IEVILDDANVDQAVEAAIKAARTDKVGDGKIFVYSVENAIRIRTGESGDEAI---- +>UniRef90_B8DJ84/1-112 +MKKIEAIIKPFKLDAVKDALIGIGVFGLTVTEVRGYGRQRGHVETYRGLEYEVQFNSKLK +IETVVPDGMSDQVVKAITTAARTGSIGDGKIFISSLEEVIRIRTGEEGTDAI---- +>UniRef90_Q6ARG9/1-112 +MKKIEAIIKPFKLEEIKEALTELAITGMTISEVKGYGRQKGHKEMYRGAEYSIDFNPKLK +IELVVRAEIADKVVEKIRLAARTGKIGDGKIFVLPIEEVVRVRTGEQGREAI---- +>UniRef90_C1W154/1-112 +MKLVTAIIQPHRLDAVKSALEAAGIRGMTVSEASGYGRQKGHTEVYRGAEYTIDLVPKIR +LEILVDDPDAHRVGEVITQAAHTGRIGDGKVWTIPVDSVTRVRTGEEGPSAL---- +>UniRef90_C1UII8/1-112 +MKLVTAIVKPFKLDDVKNALELIGIAGLTVSEVQGFGRQRGHTEVYRGAEYQVDFVPKVR +IEVVVGEIEAARVVDAIVEAASTGQIGDGKVWVTTIDEIVRVRTGERGADAL---- +>UniRef90_UPI000/1-118 +--KVTVITNQAKFYQLKTSLEAIGITGMTVIQVLGFGIQKGQPEYYRGNPIEATLLPKVK +MKKIEAIIRPEAFQTLKDGLSAVGISGLTVTEAAGCGKQQGKKGVFRGTSFEIQLV +>UniRef90_C1T022/1-113 +MKLVIAYIRPECLNAVKQELYAKKIYNMSVTNVLGSGRQKGFTETYRGVVMEVNLLKKLR +LEIGVNDDFAEQAVEAINAGARTGKEGDGVIFVLECAAAVRIRTQETGPAAMG--- +>UniRef90_Q46G48/1-112 +MKYIIAMIRPERLDAVKRELQKLEVNRLTVSSVAGYGAQKGHLEIYRATEHEANLLEKVK +IEIAVEDHFLKSVIEAIKTGAKDGYIGSGKIFVLPLENVIRIRTNETGPEAL---- +>UniRef90_A2RJQ2/1-112 +MKKIEAIIRTDKLEDLKKALSDNGVHGMTVSQVLGYGEQKGFAEYVRGQRIETTLLSKIK +IEIVSIDEKVDQIVNVITKAVRTGEVGDGKIFIQPVERVIRIRTSEEDAQAL---- +>UniRef90_Q8KF33/1-112 +MKKIEAIIRTSQYEAVKKALHEIDIDFFTWWDVTGQGNDKKHTEIYRGTVRDTSYISRRY +LSIVVRDVNLQKTVDCLIKNARTGEVGDGKIFVSDIEQSYRIRTGESGDESL---- +>UniRef90_B1HTS9/1-112 +MKKIEVIIRPEVFGAVRDGLAQQGIAGLSVSEIAGCGRQLGRTGLFRGNTYEIEFLPKLK +LEMIVDDSKVDGIVEILLREAATGKVGDGKIFIYPVEQAIRIRTKEVGSIAV---- +>UniRef90_A2SPS9/1-106 +MKMITAIIRPEKVDEVLNALEQNNIPGVTITEVLGRGEQGGVCLQYRAGKMQVKTLPKTK +LEIVVPDKDVDTLIKVIREHARTGKKGDGRIFVLPVEAAAWVRTDE---------- +>UniRef90_C0EAH3/1-111 +--KLVIVTRQSKFEELKAAMNAIEVTGMTVTQVIGCGTQKGATEFYRGVPVEMNLLPKIK +VEIVVCRVPVRTVIETAKKVLYTGHYGDGKIFVYDIENVVKVRTGEEGCAALQ--- +>UniRef90_A7I8Z1/1-104 +--MISAIIKPERFEFVKKALEDKGYVSMTITEVKGRGEQKGISLEYRGGKMTVDLLPKVK +IEIVIRDKDLEDVIATLTGAARTGKIGDGKIFVIPVEKSIRIRTGD---------- +>UniRef90_Q3AFZ0/1-114 +MKKIEALIRPQKLGEVKEALNKLGISGMTVTEVVGCGRQKGQKEIYRGIEYEINLLPKVK +IEIVTVDEKVEEIIKIISESARTGAIGDGKIFISEVLDAVRIRTGERGTAAITS-- +>UniRef90_A7I508/1-106 +MKLVIALIRPERFGAVKKALEDKGYIGMTTAEAKGRGAQKGIALVYRGGRLTIDILVKVR +IEIVSHDRDVEDLVSTIRESAWTGANGDGRIFVLPVEQAIRIRTGE---------- +>UniRef90_P51604/1-112 +MKEIIAIIRPNKINRTKEVLDALGFSSMTANAVFGRGRQKAIVGELREEEGSMRYIPKRM +ISLVVPDEDASLVVESIMKVNKTGQIGDGKIFVCPIEDAVRVRTKESGEDAI---- +>UniRef90_B0NXT3/1-112 +--KINAIVREEKFEDVKEALNKIGVNGITVSQVMGCGAQKGFTEVIRGTKVDMMMRPKIK +FEIVVSSEEWERTIEAIQKSAFTGEVGDGKIFSYEVRNVVKIRTGERDVDALQD-- +>UniRef90_A8YG01/1-96 +----------------KIALVNAGIVGMTVSEVRGFGRQKGQSERYRGSEYTVEFLQKLK +IEIVVEDKQVDMVVDKLISAARTGEIGDGKIFISPVEQIVRIRTGEKDLQAI---- +>UniRef90_C0BMJ9/1-112 +MKKVEAIIRKSKFDDVKKALHAIEVNFFSYWDVTGVGNEKQ-GHVYRGISYSTSDIQRRI +LSIVISDEFLEPTINAILEAACTGNVGDGKIFVSDVQDAYRIRTRENGKAGIN--- +>UniRef90_Q466Y2/1-112 +MCKIEAIIKPMKLHEVKDALEEAGYPSLTVTDVKGRGQQKGIVQQWRGKKYCVDLLPKTK +IEIAAPEDKIEEIIKIIQSSAYTGEIGDGKIFVTPIETVVRIRTGERNGDAL---- +>UniRef90_O26760/1-112 +MKEIVAIIRPEKLEEVKNALEAAGCHGMTVTEVRGRGRQLGITESYRGRDYRIDLLPKTK +IEIVVNDEDVDTVVETIVKSAQTGDIGDGKIFISGVDEVVRIRTGESGKKAV---- +>UniRef90_A0LYN2/1-111 +MKKIEAIIRKSEFDETKEALHSIGVTFFSYWDVTGVGNEKV-GHVYRGVSYSTADIQRRY +LSIVVTDSFVEKTVETLLKAAHTGKVGDGKIFILPVEEAYRIRTKEKGGESL---- +>UniRef90_C1YA75/1-112 +MKVVTAVIKPFKLDEVRAALLAFGVQGMTVSESSGYGRQRGHTEVYRGAEYTVELLPKVR +VEILVDDEDAEDVVDVIVRAARTGKIGDGKVWTQPVETVIRVRTGERGPEAL---- +>UniRef90_A8KX44/1-112 +MKLVTAIVRPHRVDDVRAALTTYGVHGITVSQVTGFGLEMWRTQTYRGNAFHDESTSNIR +LELVVADSDAPDVVNVIRRTAASTSSGAGKIWVLPVEGLARIRTGERGADAL---- +>UniRef90_C0EZB6/1-110 +--KLTIMCKEDRFAILKDAMSQIGVTGMTVSHVMGCGTQKGKTGQYRGVKIDMNLLPQLQ +VDIVVSTVPPELVVEAAKKALYTGEYGDGKIFLYDVENVVRIRTNETGIAAL---- +>UniRef90_Q11P32/1-112 +MKKIEAIVKPSKLKAIQAGLIKIGIPCMTVVPVKGVGLQQGFPEIYRGTEKSIVLLSKVM +IICVVSDENLEKCIDVIIETGSEGKVGDGKIFVYDVLDAIRMRTRTRGDDAI---- +>UniRef90_A7B6Y7/1-112 +--KIEAIVREEKFEQVKSALQDIQVNGVTISQVMGYGTQRGYTEIVRGSEVDILLHPKIK +FEVVVSSEEWEQTISAIQKAAFTGEVGDGKIFSYEIRSAVKIRTKETGYNAVQS-- +>UniRef90_A7VSI5/1-111 +--KVVILFNQDKFIELKDAMNAIGVTGMTVIHVMGCGVQKGNTRYYRGVKLDIVLLPKIK +LEIVVSKVPVQTV-DTARKVLYTGNIGDGKIFIYDVENVIKVRTGAEGYYALQD-- +>UniRef90_A6G036/1-110 +--KVEAMIRPFKLDDVKERLTELEVGGMTVTEVKGFGRTGGKTEFYRGSAYVIDFVPKIK +IEVVVPAARSEEVIAAIREVAASDRIGDGKIFVTPVLEAVRIRTDERGESAL---- +>UniRef90_C0ES36/1-115 +MIKVEAYVREDKFEDVKAALNAIGVNGLTVSQVMGCGIQRGYKEIVRGMQVDMQMQPKIK +FEIVVSSEEWEKTIEAIEKAAYTGEPGDGKIFTYEIRHAQKIRTKETGYDAIQAT- +>UniRef90_B5IHX8/1-113 +MKQIQAIVRPEKLDAVKDALVEIGINGITVTAVQGFGKQMGHTEVYRGVKVEAKLLTKMQ +ITSVVTDQAVDQVVQAILTAARTGEIGDGKIVITPVENAIRIRTGESGDSTLA--- +>UniRef90_B0MIE7/1-103 +---------PEKLTDVKHILEAHKVSGLMISNIMGYGNQKGFTQKYRGNELNSNLLPKIK +VESVMPEEVVEKVTKDIVNTVRTGEFGDGKIFISPVEEAIRIRTGETGKDAL---- +>UniRef90_B4S395/1-111 +MKLITAIIQEDKLDQVREALIQANISRISVSRISGHGRQE-DIDIYRGRKIAPNLRPKIK +LEIAVNEEFVDVAIDTIVDSARSGEIGDGKIFVTPLEQCVRIRTNERGGSAI---- +>UniRef90_P51254/1-112 +MKKIEAIIRPFKLNEVKLALVKGGIGGMTVVKVSGFGRQKGQTERYKGSEYSIDIIDKIK +IEIIVSDDKVNSITEIIIKTAKTGEIGDGKIFISDVEQVIRIRTNDLNSAAL---- +>UniRef90_P71524/1-104 +MKMIRAVVRPSKAEEVVDALAESGCVALTKMDVIGRGKQKG----IKIDQIYYDELPKTM +LMLVVEDDAAENVIELITKTAYTGSFGDGKIFVSPVDEAYTVRTRSCG-------- +>UniRef90_A8JI83/1-105 +---IEAIFRPWRLPFVIDTLSKYGIRGLTNTPVKGVGVQGGSRERYAGTEFGPNLVDKEK +LDIVVSRAQVDAVVRLVAASAYTGEIGDGKIFVHPVAEVVRIRTAETG-------- +>UniRef90_B0CD03/1-107 +MRTITAFIRPQQCDQVKLVLVQLGIIDITLSDVKGFGRQQGSLQQYRGSDAEIRLHRKLK +VEVKVDEEMVAPVVEKITFAARTGQVGDGKIFVSPLQKVVQVRTGEE--------- +>UniRef90_B1QY06/1-112 +MKRIEAIIRPSKLEEIKEALKNNNINGVTISQVMGCGKQLGWKEYHRGTELITNVLPKIE +VKMVIEDSKVEEVIEIISSIAKTGEVGDGKIFVIDICDCVRIRTGERGNEAL---- +>UniRef90_Q30VL0/1-106 +MKLLIAYIRPEKLSTVKKALYARGIYAMSVTNALGSGQQKGFTETYRGIVTEVNLLKKVR +IEVGVPADKAEDALAALQTGAHTGREGDGIIFVQDVARTVRVRTGE---------- +>UniRef90_A0T2Q5/1-113 +MKEVLAIIRPNMVSKTGKALEAVGFPAMTVIRCFGRGKEKGYIDAGEKLGMRMKYIPKRM +ISIVVDDADVPFVVGIIMKVNRTGKPGDGKIFVLPVEEAIRIRTGEFGVEAIG--- +>UniRef90_B3QXW9/1-112 +MKEITAIIRINKMNETKKALIKAGISSFTASRVLGRGKGQVHYDLLKGAAEGYELVSKRY +LVVVVNDNMLQPTIDAIISANQTGKPGDGKIFVSTIEDAVRVRTGETGSAIL---- +>UniRef90_B6YRQ4/1-111 +MKKIEAIIRKTRFDEVKEALLEADIEWFSYSDVRGVGKARQ-ERIYRGVVYDTSSIERIQ +INLVVRDINVEKAIKAIEKSAHTGEVGDGRIFVSTIDNAYSIRTGEQGDETL---- +>UniRef90_B0MJN0/1-114 +MTKVDIIANQEKFEVLKHALSSIGITGMTVSHVMGCGMQKGSTEFYRGVPVDARLLPKMK +VEIVVCKVPVEKVVEVAKNALYTGKIGDGKIFVYDVENVIKVRTGEEAYEALQD-- +>UniRef90_C2C1T3/1-112 +--KIEIITRPNRFDVFQKALKEIGVSGLTVTKAVGTGLEKGMIELYRGTIKENNVHERMK +VEIVVSTVPVEAVLEVVKNTLRTGEPGDGKVFVYPLSDVIKISTGEHGVAALQD-- +>UniRef90_C1VTA2/1-110 +--LVMAIVRPEKLSDVKAALAEAGAPSLTVTQVSGRGSQPAKTGQWRGEEYVIDLHQKIK +VECVVEPEDADDVVEAIREGANTGEKGDGKIFVLPVFDAVQVRTGDRGTDAI---- +>UniRef90_A3XNG5/1-112 +MKKIEAIIRKSKFTAVKKALHDKGVNFFSYWDVTGLGNEKE-GHVYRGVSYSTSDIQRRY +LSIVVNDDFEQAAVAAILDAAATGEVGDGKIFVSDVQDAYRIRTGKKGPDTLN--- +>UniRef90_P71525/1-111 +MKEIIAIIRPSKMAQTKTVLEGLGFPAMTANRVLGRGKQKAIVGELGFEV-DMRYIPKTM +LTLIVPDEDASLVVEAIMKVNKSGQYGDGKIFVCPIEDIITVRTSERGEAAI---- +>UniRef90_Q46C91/1-112 +MKEIIAIIRPKKVVPTKEALEKLGVPSLTAIPVFGRGKQKGIATELDIAGRRMEYIPKRL +FSIVTRNEDVDTIIETIMKVNQTGDIGDGRIFICPVDDAIRVRTDEHGDNAL---- +>UniRef90_B7BWA8/1-112 +MKEVMIILRPKMYFPTKDALDQAGFHSMTIREIIGRGKCPVHYDYDEGAPVKHRLVAKRM +IDMFVRDEDLQKLIDTVVEVNKTNHAGDGKIFVLPVNDAIRVRTGEKGIEAI---- +>UniRef90_Q7UGU6/1-112 +MKLIIAIVQPSKLDAIKEALTRVEVHRLTVVDCQGFGRQRGQTGSMRGRDYGVSLLRKVQ +LQIGVNEEFVQPTIDAIGRSGESGEIGDGKIFVLPMDDCVRIRTGERGGEAI---- +>UniRef90_A3HVG6/1-112 +MKKIEAIIRTSRFEQIHSCVAGLGVKFLTFYEVKGMGLEHAKQQTYRGVAYEPTYIPRTK +LEIVTVDELVEPVINCILTEGKTGEVGDGKIFVYDVLEAHRIRNNDQGEQAL---- +>UniRef90_A0YMH7/1-112 +MKRIEALIRPVQFDSVVTALVEAGIVGMSVTNVRGYGRQKGQTESYRGVKHVIEFHPKMK +LEIVVEDEVCEFVVEKLVEAAQTGQIGDGKIFIQSMEHIIRTRTGESDLEAL---- +>UniRef90_Q46A23/1-112 +MKYIIAMIRPEKLDSVKKEIQKIGAHGLTVSSISGYGAQGGHLNVDRTKKYEANLLDKVK +IEIAVKDEFLQTTVEAIERGSKDGYIGSGKIFVLPLENVMRIRTKETGNDAL---- +>UniRef90_B4VJP7/1-90 +----------------MKALLDAGYPAVTKVDVFGRGKQRG----LKIGNVLYDELPKAL +LMVVVPDTEKEFVIRAILSSARTGAEGDGKIFVSPVEEVYTISSGKTDSS------ +>UniRef90_B1QUW3/1-103 +MYLVRAIIRTEKVNGVLSELVDAGFPQVTKMDVFGRGKQKG----IQVGEVHYDELPKEM +LLIVVKDEDKDDVVRVIMKNSRTGEYGDGKIFISKVDTAYTISTGKE--------- +>UniRef90_A5N1U1/1-112 +MKEIMAVIRMNMVGKTKKALAENGFPSITCKDVLGRGKKMVEEELHRIEDESYRLISKRL +IWILAKDEDVKKIADIIIDINQTGHPGDGKIFVTKVTDVVRIRTGETQDEAV---- +>UniRef90_A9D1T1/1-65 +-----------------------------------------------GAEYMVDFLPKVK +IELVIQDELLDRAIEVIVDTARTGKIGDGKIFVTEIERVIRIRTGEENEEAV---- +>UniRef90_A6LUZ0/1-104 +MYMIRAIIRPERVSTVLSELLDAGFPEVTKMAVYGRGKQKG----IKVGEVYYDELPKEM +LLIAVKDEDKDDVIKVIIRNSRTGEFGDGKIFVAPIEEVYTVSSGKSG-------- +>UniRef90_A6LUZ1/1-112 +MKEVMCIIRLNKVNKTKEALAEAGFPSITCRKVLGRGKKSALVEAYMETGEVPRLIPKRF +ITLVVKDDEVKTVVDTVISVNSTGTPGDGKIFVLPVEEVYRVRDGQIGEEAI---- +>UniRef90_B8GEW5/1-112 +MKEIMAIVRMKKTGVTKRALVETGVAGFTALKVLGRGKLVEDTAVIEPAEQEVRFFPRRL +FTILAHDEDVPRIVEAITKVNITEKVGDGIILVLPVDDAVRVRTGESGDAAI---- +>UniRef90_C1FI34/1-109 +--QVRAMVRPWRLSGVIDALNKYGIRGLTTYTVHGAGVQIGTVERYAGSTFDANLVEKVV +VEIVVVREQCQEVVDVIVDAAQTGEIGDGKIFLSPVHDIVRIRTGEVGAAA----- +>UniRef90_C1TA34/1-112 +MKEIIAIIRMNKVNITKKALADVGVCGLHAIKVMGRGKQLGVREEIDGLSGGTRLIPKRL +LTILARDEDVKKIVDTVIKVNQEGNKGDGRIFIAPVIDAYRVRTAEKGEAAV---- +>UniRef90_C1T440/1-112 +MKEVIAVIRMNMMNKTKKALQDAGVVAFFAHEAFGRGKGLVDVKPLEGARKGIELYPKRM +LTVVVTDDLVPEVVKVITDTNKTGQPGDGKIFVLPMIDAVRVRTGEKGAKSI---- +>UniRef90_A9A2H4/1-100 +MKKVEAIVNESAQNAVIDAMRKVGISGVTVSKVQGQGAQD--------PPLVGDFFSRVL +IVCVVDDPKLDEILDAIAGAACTGTKGDGKVYVSDICDALDICTKKRG-------- +>UniRef90_Q97ME3/1-112 +MKEIMAIIRMNMVEKTKEALLKGGNPAITCLKVLGRGRQKVDIEDYKMAEELSELISKRL +IIILAKDEDVKEIVDEIIEVNRTGNPGDGKIFVINIADAMRIRTEETGDMAI---- diff --git a/binaries/src/jpred/tests/alignment.msf b/binaries/src/jpred/tests/alignment.msf new file mode 100644 index 0000000..8fc3fec --- /dev/null +++ b/binaries/src/jpred/tests/alignment.msf @@ -0,0 +1,372 @@ + +NoName MSF: 89 Type: P Thu Sep 12 11:18:51 2013 Check: 00 .. + + Name: QUERY/1-116 Len: 116 Check: 2040 Weight: 1.00 + Name: UniRef90_C0EK60/1-112 Len: 116 Check: 9351 Weight: 1.00 + Name: UniRef90_Q21P81/1-112 Len: 116 Check: 1134 Weight: 1.00 + Name: UniRef90_Q47GI8/1-112 Len: 116 Check: 2374 Weight: 1.00 + Name: UniRef90_B9ZJ79/1-112 Len: 116 Check: 961 Weight: 1.00 + Name: UniRef90_B5FAN6/1-112 Len: 116 Check: 1022 Weight: 1.00 + Name: UniRef90_B5ZIL8/1-112 Len: 116 Check: 8167 Weight: 1.00 + Name: UniRef90_B4RVM6/1-112 Len: 116 Check: 1597 Weight: 1.00 + Name: UniRef90_B2FHB8/1-112 Len: 116 Check: 923 Weight: 1.00 + Name: UniRef90_P21193/1-112 Len: 116 Check: 482 Weight: 1.00 + Name: UniRef90_B5JS45/1-112 Len: 116 Check: 1397 Weight: 1.00 + Name: UniRef90_Q07UM0/1-112 Len: 116 Check: 2895 Weight: 1.00 + Name: UniRef90_Q2RVB4/1-112 Len: 116 Check: 2212 Weight: 1.00 + Name: UniRef90_A9IPV3/1-112 Len: 116 Check: 462 Weight: 1.00 + Name: UniRef90_A4TZT2/1-112 Len: 116 Check: 565 Weight: 1.00 + Name: UniRef90_B3DVA4/1-110 Len: 116 Check: 6589 Weight: 1.00 + Name: UniRef90_C1STD4/1-112 Len: 116 Check: 1985 Weight: 1.00 + Name: UniRef90_A7HGG9/1-112 Len: 116 Check: 1807 Weight: 1.00 + Name: UniRef90_A9BCF1/1-112 Len: 116 Check: 3971 Weight: 1.00 + Name: UniRef90_B4U911/1-112 Len: 116 Check: 2943 Weight: 1.00 + Name: UniRef90_B1ZSX2/1-112 Len: 116 Check: 431 Weight: 1.00 + Name: UniRef90_Q7X1L4/1-112 Len: 116 Check: 4218 Weight: 1.00 + Name: UniRef90_Q1NW36/1-112 Len: 116 Check: 2273 Weight: 1.00 + Name: UniRef90_C0GRX0/1-112 Len: 116 Check: 8886 Weight: 1.00 + Name: UniRef90_B8DJ84/1-112 Len: 116 Check: 3489 Weight: 1.00 + Name: UniRef90_Q6ARG9/1-112 Len: 116 Check: 1309 Weight: 1.00 + Name: UniRef90_C1W154/1-112 Len: 116 Check: 5141 Weight: 1.00 + Name: UniRef90_C1UII8/1-112 Len: 116 Check: 3484 Weight: 1.00 + Name: UniRef90_UPI000/1-118 Len: 120 Check: 2455 Weight: 1.00 + Name: UniRef90_C1T022/1-113 Len: 116 Check: 6949 Weight: 1.00 + Name: UniRef90_Q46G48/1-112 Len: 116 Check: 1089 Weight: 1.00 + Name: UniRef90_A2RJQ2/1-112 Len: 116 Check: 4156 Weight: 1.00 + Name: UniRef90_Q8KF33/1-112 Len: 116 Check: 5483 Weight: 1.00 + Name: UniRef90_B1HTS9/1-112 Len: 116 Check: 1444 Weight: 1.00 + Name: UniRef90_A2SPS9/1-106 Len: 116 Check: 9791 Weight: 1.00 + Name: UniRef90_C0EAH3/1-111 Len: 116 Check: 3946 Weight: 1.00 + Name: UniRef90_A7I8Z1/1-104 Len: 116 Check: 5077 Weight: 1.00 + Name: UniRef90_Q3AFZ0/1-114 Len: 116 Check: 441 Weight: 1.00 + Name: UniRef90_A7I508/1-106 Len: 116 Check: 7683 Weight: 1.00 + Name: UniRef90_P51604/1-112 Len: 116 Check: 1016 Weight: 1.00 + Name: UniRef90_B0NXT3/1-112 Len: 116 Check: 7617 Weight: 1.00 + Name: UniRef90_A8YG01/1-96 Len: 116 Check: 8909 Weight: 1.00 + Name: UniRef90_C0BMJ9/1-112 Len: 116 Check: 4293 Weight: 1.00 + Name: UniRef90_Q466Y2/1-112 Len: 116 Check: 4079 Weight: 1.00 + Name: UniRef90_O26760/1-112 Len: 116 Check: 3785 Weight: 1.00 + Name: UniRef90_A0LYN2/1-111 Len: 116 Check: 804 Weight: 1.00 + Name: UniRef90_C1YA75/1-112 Len: 116 Check: 6435 Weight: 1.00 + Name: UniRef90_A8KX44/1-112 Len: 116 Check: 4614 Weight: 1.00 + Name: UniRef90_C0EZB6/1-110 Len: 116 Check: 179 Weight: 1.00 + Name: UniRef90_Q11P32/1-112 Len: 116 Check: 3377 Weight: 1.00 + Name: UniRef90_A7B6Y7/1-112 Len: 116 Check: 676 Weight: 1.00 + Name: UniRef90_A7VSI5/1-111 Len: 116 Check: 5848 Weight: 1.00 + Name: UniRef90_A6G036/1-110 Len: 116 Check: 8450 Weight: 1.00 + Name: UniRef90_C0ES36/1-115 Len: 116 Check: 1154 Weight: 1.00 + Name: UniRef90_B5IHX8/1-113 Len: 116 Check: 7450 Weight: 1.00 + Name: UniRef90_B0MIE7/1-103 Len: 116 Check: 2131 Weight: 1.00 + Name: UniRef90_B4S395/1-111 Len: 116 Check: 8256 Weight: 1.00 + Name: UniRef90_P51254/1-112 Len: 116 Check: 2366 Weight: 1.00 + Name: UniRef90_P71524/1-104 Len: 116 Check: 2281 Weight: 1.00 + Name: UniRef90_A8JI83/1-105 Len: 116 Check: 84 Weight: 1.00 + Name: UniRef90_B0CD03/1-107 Len: 116 Check: 5133 Weight: 1.00 + Name: UniRef90_B1QY06/1-112 Len: 116 Check: 1778 Weight: 1.00 + Name: UniRef90_Q30VL0/1-106 Len: 116 Check: 975 Weight: 1.00 + Name: UniRef90_A0T2Q5/1-113 Len: 116 Check: 3875 Weight: 1.00 + Name: UniRef90_B3QXW9/1-112 Len: 116 Check: 2335 Weight: 1.00 + Name: UniRef90_B6YRQ4/1-111 Len: 116 Check: 320 Weight: 1.00 + Name: UniRef90_B0MJN0/1-114 Len: 116 Check: 2340 Weight: 1.00 + Name: UniRef90_C2C1T3/1-112 Len: 116 Check: 7783 Weight: 1.00 + Name: UniRef90_C1VTA2/1-110 Len: 116 Check: 8079 Weight: 1.00 + Name: UniRef90_A3XNG5/1-112 Len: 116 Check: 4563 Weight: 1.00 + Name: UniRef90_P71525/1-111 Len: 116 Check: 6955 Weight: 1.00 + Name: UniRef90_Q46C91/1-112 Len: 116 Check: 9645 Weight: 1.00 + Name: UniRef90_B7BWA8/1-112 Len: 116 Check: 484 Weight: 1.00 + Name: UniRef90_Q7UGU6/1-112 Len: 116 Check: 2772 Weight: 1.00 + Name: UniRef90_A3HVG6/1-112 Len: 116 Check: 3382 Weight: 1.00 + Name: UniRef90_A0YMH7/1-112 Len: 116 Check: 3597 Weight: 1.00 + Name: UniRef90_Q46A23/1-112 Len: 116 Check: 2151 Weight: 1.00 + Name: UniRef90_B4VJP7/1-90 Len: 116 Check: 2329 Weight: 1.00 + Name: UniRef90_B1QUW3/1-103 Len: 116 Check: 8604 Weight: 1.00 + Name: UniRef90_A5N1U1/1-112 Len: 116 Check: 2241 Weight: 1.00 + Name: UniRef90_A9D1T1/1-65 Len: 116 Check: 8348 Weight: 1.00 + Name: UniRef90_A6LUZ0/1-104 Len: 116 Check: 2978 Weight: 1.00 + Name: UniRef90_A6LUZ1/1-112 Len: 116 Check: 3539 Weight: 1.00 + Name: UniRef90_B8GEW5/1-112 Len: 116 Check: 751 Weight: 1.00 + Name: UniRef90_C1FI34/1-109 Len: 116 Check: 3899 Weight: 1.00 + Name: UniRef90_C1TA34/1-112 Len: 116 Check: 116 Weight: 1.00 + Name: UniRef90_C1T440/1-112 Len: 116 Check: 857 Weight: 1.00 + Name: UniRef90_A9A2H4/1-100 Len: 116 Check: 7883 Weight: 1.00 + Name: UniRef90_Q97ME3/1-112 Len: 116 Check: 8399 Weight: 1.00 + +// + + + 1 50 +QUERY/1-116 MKKIEAIIRP FKLDEVKIAL VNAGIVGMTV SEVRGFGRQK GQTERYRGSE +UniRef90_C0EK60/1-112 MKKIEAIIKP FKLDDVREIL TEIGITGMTV SEVKGFGRQK GHTEIYRGAE +UniRef90_Q21P81/1-112 MKLITAVIKP FKLDDVRNAL SEIGVQGMTV TEVKGFGRQK GHTELYRGAE +UniRef90_Q47GI8/1-112 MKKIEAIIKP FKLDEVREAL SEIGISGLTV TEVKGFGRQK GHTELYRGAE +UniRef90_B9ZJ79/1-112 MKKIEAIIKP FKLEDVREAL TEMGIAGMTA TEVQGFGRQK GHTELYRGAE +UniRef90_B5FAN6/1-112 MKIINAIIKP FKLDDVREAL ADAGVDGMTV SEVKGFGRQK GHTELYRGAE +UniRef90_B5ZIL8/1-112 MKKIEAIIKP FKLDEVKDAL HEIGLMGISV TEAKGFGRQK GHTELYRGAE +UniRef90_B4RVM6/1-112 MKKIEAIIKP FKMDDVREAL AEVGIAGMTV SEVKGFGRQK GHTELYRGAE +UniRef90_B2FHB8/1-112 MKLISAIIRP FKLDEVREAL SDAGVSGITV TEVKGFGRQK GHTELYRGAE +UniRef90_P21193/1-112 MKKIEAIIKP FKLDEVKEAL HEVGIKGITV TEAKGFGRQK GHTELYRGAE +UniRef90_B5JS45/1-112 MKKIEAVIKP FKLDDVRDAL ADIGVSGMTV TEVKGFGRQK GHTETYRGAE +UniRef90_Q07UM0/1-112 MKLVVAIIKP FKLDEVRQAL TDVGVHGMTV TEVKGYGRQR GHTEIYRGAE +UniRef90_Q2RVB4/1-112 MKFVIAITKP FKLDEVREAL GALGIQGMTV TEVKGFGRQK GQTEVYRGAE +UniRef90_A9IPV3/1-112 MKLIIAIIKP FKLDEVRVAL SGIGVQGLTV TEVKGFGRQK GHTELYRGAE +UniRef90_A4TZT2/1-112 MKLIIAIIKP FKLDEVREAL TQLGIQGLTA TEVKGFGRQK GQTEIYRAAE +UniRef90_B3DVA4/1-110 --KIEAIIKP FKLEEVKEAL TEIGIAGLTV TEVKGFGRQK GHTEIYRGSE +UniRef90_C1STD4/1-112 MRKIEIITRP FKLDEVKQRL TKLGIQGMTV TEVKGFGRQR GHKEIYRGAE +UniRef90_A7HGG9/1-112 MKRIEAIIRP SKLEDVRRLL SHPWISAMTV SEVRGAGRQK GHAELYRGAE +UniRef90_A9BCF1/1-112 MKKIEAIIRP FKLEDVKVAL VNSGIVGMTV SEVRGFGRQK GQVERYRGSE +UniRef90_B4U911/1-112 MKKVEAIIKP FKLDEVKDAL VEIGIGGMTI TEVKGFGQQK GKTEIYRATE +UniRef90_B1ZSX2/1-112 MKLVTAIIKP FKLEEIKAAL AEIQVEGMTV TEVKGFGRQK GHTEIYRGTE +UniRef90_Q7X1L4/1-112 MKKVEAIIKP FKLDAVKEAV TALGVYGMTV TEVKGYGQQK GHTEQYRGAE +UniRef90_Q1NW36/1-112 MKKVEAIIKP FKLDAVKEAV TALGIHGMTV SEVKGFGRQK GHTEVYRGAE +UniRef90_C0GRX0/1-112 MKKLEIITRP FKVEAVKEAL AGMGIKGMTL TDVKGFGRQM GHKEIYRGAE +UniRef90_B8DJ84/1-112 MKKIEAIIKP FKLDAVKDAL IGIGVFGLTV TEVRGYGRQR GHVETYRGLE +UniRef90_Q6ARG9/1-112 MKKIEAIIKP FKLEEIKEAL TELAITGMTI SEVKGYGRQK GHKEMYRGAE +UniRef90_C1W154/1-112 MKLVTAIIQP HRLDAVKSAL EAAGIRGMTV SEASGYGRQK GHTEVYRGAE +UniRef90_C1UII8/1-112 MKLVTAIVKP FKLDDVKNAL ELIGIAGLTV SEVQGFGRQR GHTEVYRGAE +UniRef90_UPI000/1-118 --KVTVITNQ AKFYQLKTSL EAIGITGMTV IQVLGFGIQK GQPEYYRGNP +UniRef90_C1T022/1-113 MKLVIAYIRP ECLNAVKQEL YAKKIYNMSV TNVLGSGRQK GFTETYRGVV +UniRef90_Q46G48/1-112 MKYIIAMIRP ERLDAVKREL QKLEVNRLTV SSVAGYGAQK GHLEIYRATE +UniRef90_A2RJQ2/1-112 MKKIEAIIRT DKLEDLKKAL SDNGVHGMTV SQVLGYGEQK GFAEYVRGQR +UniRef90_Q8KF33/1-112 MKKIEAIIRT SQYEAVKKAL HEIDIDFFTW WDVTGQGNDK KHTEIYRGTV +UniRef90_B1HTS9/1-112 MKKIEVIIRP EVFGAVRDGL AQQGIAGLSV SEIAGCGRQL GRTGLFRGNT +UniRef90_A2SPS9/1-106 MKMITAIIRP EKVDEVLNAL EQNNIPGVTI TEVLGRGEQG GVCLQYRAGK +UniRef90_C0EAH3/1-111 --KLVIVTRQ SKFEELKAAM NAIEVTGMTV TQVIGCGTQK GATEFYRGVP +UniRef90_A7I8Z1/1-104 --MISAIIKP ERFEFVKKAL EDKGYVSMTI TEVKGRGEQK GISLEYRGGK +UniRef90_Q3AFZ0/1-114 MKKIEALIRP QKLGEVKEAL NKLGISGMTV TEVVGCGRQK GQKEIYRGIE +UniRef90_A7I508/1-106 MKLVIALIRP ERFGAVKKAL EDKGYIGMTT AEAKGRGAQK GIALVYRGGR +UniRef90_P51604/1-112 MKEIIAIIRP NKINRTKEVL DALGFSSMTA NAVFGRGRQK AIVGELREEE +UniRef90_B0NXT3/1-112 --KINAIVRE EKFEDVKEAL NKIGVNGITV SQVMGCGAQK GFTEVIRGTK +UniRef90_A8YG01/1-96 ---------- ------KIAL VNAGIVGMTV SEVRGFGRQK GQSERYRGSE +UniRef90_C0BMJ9/1-112 MKKVEAIIRK SKFDDVKKAL HAIEVNFFSY WDVTGVGNEK Q-GHVYRGIS +UniRef90_Q466Y2/1-112 MCKIEAIIKP MKLHEVKDAL EEAGYPSLTV TDVKGRGQQK GIVQQWRGKK +UniRef90_O26760/1-112 MKEIVAIIRP EKLEEVKNAL EAAGCHGMTV TEVRGRGRQL GITESYRGRD +UniRef90_A0LYN2/1-111 MKKIEAIIRK SEFDETKEAL HSIGVTFFSY WDVTGVGNEK V-GHVYRGVS +UniRef90_C1YA75/1-112 MKVVTAVIKP FKLDEVRAAL LAFGVQGMTV SESSGYGRQR GHTEVYRGAE +UniRef90_A8KX44/1-112 MKLVTAIVRP HRVDDVRAAL TTYGVHGITV SQVTGFGLEM WRTQTYRGNA +UniRef90_C0EZB6/1-110 --KLTIMCKE DRFAILKDAM SQIGVTGMTV SHVMGCGTQK GKTGQYRGVK +UniRef90_Q11P32/1-112 MKKIEAIVKP SKLKAIQAGL IKIGIPCMTV VPVKGVGLQQ GFPEIYRGTE +UniRef90_A7B6Y7/1-112 --KIEAIVRE EKFEQVKSAL QDIQVNGVTI SQVMGYGTQR GYTEIVRGSE +UniRef90_A7VSI5/1-111 --KVVILFNQ DKFIELKDAM NAIGVTGMTV IHVMGCGVQK GNTRYYRGVK +UniRef90_A6G036/1-110 --KVEAMIRP FKLDDVKERL TELEVGGMTV TEVKGFGRTG GKTEFYRGSA +UniRef90_C0ES36/1-115 MIKVEAYVRE DKFEDVKAAL NAIGVNGLTV SQVMGCGIQR GYKEIVRGMQ +UniRef90_B5IHX8/1-113 MKQIQAIVRP EKLDAVKDAL VEIGINGITV TAVQGFGKQM GHTEVYRGVK +UniRef90_B0MIE7/1-103 ---------P EKLTDVKHIL EAHKVSGLMI SNIMGYGNQK GFTQKYRGNE +UniRef90_B4S395/1-111 MKLITAIIQE DKLDQVREAL IQANISRISV SRISGHGRQE -DIDIYRGRK +UniRef90_P51254/1-112 MKKIEAIIRP FKLNEVKLAL VKGGIGGMTV VKVSGFGRQK GQTERYKGSE +UniRef90_P71524/1-104 MKMIRAVVRP SKAEEVVDAL AESGCVALTK MDVIGRGKQK G----IKIDQ +UniRef90_A8JI83/1-105 ---IEAIFRP WRLPFVIDTL SKYGIRGLTN TPVKGVGVQG GSRERYAGTE +UniRef90_B0CD03/1-107 MRTITAFIRP QQCDQVKLVL VQLGIIDITL SDVKGFGRQQ GSLQQYRGSD +UniRef90_B1QY06/1-112 MKRIEAIIRP SKLEEIKEAL KNNNINGVTI SQVMGCGKQL GWKEYHRGTE +UniRef90_Q30VL0/1-106 MKLLIAYIRP EKLSTVKKAL YARGIYAMSV TNALGSGQQK GFTETYRGIV +UniRef90_A0T2Q5/1-113 MKEVLAIIRP NMVSKTGKAL EAVGFPAMTV IRCFGRGKEK GYIDAGEKLG +UniRef90_B3QXW9/1-112 MKEITAIIRI NKMNETKKAL IKAGISSFTA SRVLGRGKGQ VHYDLLKGAA +UniRef90_B6YRQ4/1-111 MKKIEAIIRK TRFDEVKEAL LEADIEWFSY SDVRGVGKAR Q-ERIYRGVV +UniRef90_B0MJN0/1-114 MTKVDIIANQ EKFEVLKHAL SSIGITGMTV SHVMGCGMQK GSTEFYRGVP +UniRef90_C2C1T3/1-112 --KIEIITRP NRFDVFQKAL KEIGVSGLTV TKAVGTGLEK GMIELYRGTI +UniRef90_C1VTA2/1-110 --LVMAIVRP EKLSDVKAAL AEAGAPSLTV TQVSGRGSQP AKTGQWRGEE +UniRef90_A3XNG5/1-112 MKKIEAIIRK SKFTAVKKAL HDKGVNFFSY WDVTGLGNEK E-GHVYRGVS +UniRef90_P71525/1-111 MKEIIAIIRP SKMAQTKTVL EGLGFPAMTA NRVLGRGKQK AIVGELGFEV +UniRef90_Q46C91/1-112 MKEIIAIIRP KKVVPTKEAL EKLGVPSLTA IPVFGRGKQK GIATELDIAG +UniRef90_B7BWA8/1-112 MKEVMIILRP KMYFPTKDAL DQAGFHSMTI REIIGRGKCP VHYDYDEGAP +UniRef90_Q7UGU6/1-112 MKLIIAIVQP SKLDAIKEAL TRVEVHRLTV VDCQGFGRQR GQTGSMRGRD +UniRef90_A3HVG6/1-112 MKKIEAIIRT SRFEQIHSCV AGLGVKFLTF YEVKGMGLEH AKQQTYRGVA +UniRef90_A0YMH7/1-112 MKRIEALIRP VQFDSVVTAL VEAGIVGMSV TNVRGYGRQK GQTESYRGVK +UniRef90_Q46A23/1-112 MKYIIAMIRP EKLDSVKKEI QKIGAHGLTV SSISGYGAQG GHLNVDRTKK +UniRef90_B4VJP7/1-90 ---------- ------MKAL LDAGYPAVTK VDVFGRGKQR G----LKIGN +UniRef90_B1QUW3/1-103 MYLVRAIIRT EKVNGVLSEL VDAGFPQVTK MDVFGRGKQK G----IQVGE +UniRef90_A5N1U1/1-112 MKEIMAVIRM NMVGKTKKAL AENGFPSITC KDVLGRGKKM VEEELHRIED +UniRef90_A9D1T1/1-65 ---------- ---------- ---------- ---------- -------GAE +UniRef90_A6LUZ0/1-104 MYMIRAIIRP ERVSTVLSEL LDAGFPEVTK MAVYGRGKQK G----IKVGE +UniRef90_A6LUZ1/1-112 MKEVMCIIRL NKVNKTKEAL AEAGFPSITC RKVLGRGKKS ALVEAYMETG +UniRef90_B8GEW5/1-112 MKEIMAIVRM KKTGVTKRAL VETGVAGFTA LKVLGRGKLV EDTAVIEPAE +UniRef90_C1FI34/1-109 --QVRAMVRP WRLSGVIDAL NKYGIRGLTT YTVHGAGVQI GTVERYAGST +UniRef90_C1TA34/1-112 MKEIIAIIRM NKVNITKKAL ADVGVCGLHA IKVMGRGKQL GVREEIDGLS +UniRef90_C1T440/1-112 MKEVIAVIRM NMMNKTKKAL QDAGVVAFFA HEAFGRGKGL VDVKPLEGAR +UniRef90_A9A2H4/1-100 MKKVEAIVNE SAQNAVIDAM RKVGISGVTV SKVQGQGAQD --------PP +UniRef90_Q97ME3/1-112 MKEIMAIIRM NMVEKTKEAL LKGGNPAITC LKVLGRGRQK VDIEDYKMAE + + + 51 100 +QUERY/1-116 YTVEFLQKLK LEIVVEDAQV DTVIDKIVAA ARTGENGDGK IFVSPVDQTI +UniRef90_C0EK60/1-112 YAVDFLPKVK IELVLADDKV DQAVDAILET AHSGKIGDGK IFIYPVEEAI +UniRef90_Q21P81/1-112 YVIDFLPKVK LELVLGDELI DQAVEAISKA AQTGKIGDGK IFITPCEEVI +UniRef90_Q47GI8/1-112 YVVDFLPKIK IEIVVNSNNV EPAIDAIIKA ARTGKIGDGK IFVMPVEQVV +UniRef90_B9ZJ79/1-112 YVVDFLPKVK LELVVDDDRV DACIDAIVKA SRTGKIGDGK IFVSDMARVV +UniRef90_B5FAN6/1-112 YQVDFLPKVK LEIAVQAEGV DRIVEAISKA AHTGKIGDGK IFVYDLQQAV +UniRef90_B5ZIL8/1-112 YIVDFLPKVK LEIVCADNLV DRAVETIMAA ARTGRIGDGK IFILPVEDVI +UniRef90_B4RVM6/1-112 YQVDFLPKIK IELVLDDDRV EQAVEAIQSS AKTGKIGDGK IFVYSVESAV +UniRef90_B2FHB8/1-112 YVVDFLPKIK IETVVTDERA DAVIEAIQSS AGTGKIGDGK IFVTAVEQVI +UniRef90_P21193/1-112 YVVDFLPKVK IEVVMEDSLV ERAIEAIQQA AHTGRIGDGK IFVTPVEEVV +UniRef90_B5JS45/1-112 YVVDFLPKLK LEIVVAEKDA DACVESITNA AKTGQIGDGK IFVSDVERTI +UniRef90_Q07UM0/1-112 YLVNFLPKLR IEVGVADTLV DKAVEAITRS ARTGQIGDGK IFVTPLDHAL +UniRef90_Q2RVB4/1-112 YVVNFLPKVK IELAVPDNLL DQVVETIQST AQTGKIGDGK IFVFDLGEAV +UniRef90_A9IPV3/1-112 YAVDFLPKLR VEAAVPDHLV DQVIDVIEQA ARTGKIGDGK IFTAPLEQVI +UniRef90_A4TZT2/1-112 YVVSFVPKIK IELVVNDDVV DRAVEAIQAA ARTDKIGDGK IFVMDVAHAL +UniRef90_B3DVA4/1-110 YTVDFLPKVK VEIVLTEDIL PKAVEAIIKS AKTGKIGDGK IFVLPVSEAI +UniRef90_C1STD4/1-112 YQVDFVAKVK IEIVVDDGLV EEIVSTVQEG ARTGKVGDGK IFISPVDNAV +UniRef90_A7HGG9/1-112 YVIDLIPKLK LEIVLPDPLV DRVVADLESW LRTGRIGDGK IFVEPLDDAV +UniRef90_A9BCF1/1-112 FTVEFLQKLK IEIVVADESV PTVLTAIAEA AKTGEIGDGK IFISPVESVV +UniRef90_B4U911/1-112 YVIDFLPKIK IETVVKDSEV EKVVQTILKS AQTGKVGDGK IFIYNVEETV +UniRef90_B1ZSX2/1-112 YTVDFLPKVR IEILAADESV PKILETIIST AKTGKIGDGK IFISAAEDVV +UniRef90_Q7X1L4/1-112 YVVEFITKIK VEIVVADAKV SPVLEAIRRT AMSNSIGDGK VFVSPVETAL +UniRef90_Q1NW36/1-112 YVVDFVAKIK VEIVVESEKA SLLVETITQA ARNGNIGDGK IFVTPVESVC +UniRef90_C0GRX0/1-112 YDVDFLPKVK IEVILDDANV DQAVEAAIKA ARTDKVGDGK IFVYSVENAI +UniRef90_B8DJ84/1-112 YEVQFNSKLK IETVVPDGMS DQVVKAITTA ARTGSIGDGK IFISSLEEVI +UniRef90_Q6ARG9/1-112 YSIDFNPKLK IELVVRAEIA DKVVEKIRLA ARTGKIGDGK IFVLPIEEVV +UniRef90_C1W154/1-112 YTIDLVPKIR LEILVDDPDA HRVGEVITQA AHTGRIGDGK VWTIPVDSVT +UniRef90_C1UII8/1-112 YQVDFVPKVR IEVVVGEIEA ARVVDAIVEA ASTGQIGDGK VWVTTIDEIV +UniRef90_UPI000/1-118 IEATLLPKVK MKKIEAIIRP EAFQTLKDGL SAVGISGLTV TEAAGCGKQQ +UniRef90_C1T022/1-113 MEVNLLKKLR LEIGVNDDFA EQAVEAINAG ARTGKEGDGV IFVLECAAAV +UniRef90_Q46G48/1-112 HEANLLEKVK IEIAVEDHFL KSVIEAIKTG AKDGYIGSGK IFVLPLENVI +UniRef90_A2RJQ2/1-112 IETTLLSKIK IEIVSIDEKV DQIVNVITKA VRTGEVGDGK IFIQPVERVI +UniRef90_Q8KF33/1-112 RDTSYISRRY LSIVVRDVNL QKTVDCLIKN ARTGEVGDGK IFVSDIEQSY +UniRef90_B1HTS9/1-112 YEIEFLPKLK LEMIVDDSKV DGIVEILLRE AATGKVGDGK IFIYPVEQAI +UniRef90_A2SPS9/1-106 MQVKTLPKTK LEIVVPDKDV DTLIKVIREH ARTGKKGDGR IFVLPVEAAA +UniRef90_C0EAH3/1-111 VEMNLLPKIK VEIVVCRVPV RTVIETAKKV LYTGHYGDGK IFVYDIENVV +UniRef90_A7I8Z1/1-104 MTVDLLPKVK IEIVIRDKDL EDVIATLTGA ARTGKIGDGK IFVIPVEKSI +UniRef90_Q3AFZ0/1-114 YEINLLPKVK IEIVTVDEKV EEIIKIISES ARTGAIGDGK IFISEVLDAV +UniRef90_A7I508/1-106 LTIDILVKVR IEIVSHDRDV EDLVSTIRES AWTGANGDGR IFVLPVEQAI +UniRef90_P51604/1-112 GSMRYIPKRM ISLVVPDEDA SLVVESIMKV NKTGQIGDGK IFVCPIEDAV +UniRef90_B0NXT3/1-112 VDMMMRPKIK FEIVVSSEEW ERTIEAIQKS AFTGEVGDGK IFSYEVRNVV +UniRef90_A8YG01/1-96 YTVEFLQKLK IEIVVEDKQV DMVVDKLISA ARTGEIGDGK IFISPVEQIV +UniRef90_C0BMJ9/1-112 YSTSDIQRRI LSIVISDEFL EPTINAILEA ACTGNVGDGK IFVSDVQDAY +UniRef90_Q466Y2/1-112 YCVDLLPKTK IEIAAPEDKI EEIIKIIQSS AYTGEIGDGK IFVTPIETVV +UniRef90_O26760/1-112 YRIDLLPKTK IEIVVNDEDV DTVVETIVKS AQTGDIGDGK IFISGVDEVV +UniRef90_A0LYN2/1-111 YSTADIQRRY LSIVVTDSFV EKTVETLLKA AHTGKVGDGK IFILPVEEAY +UniRef90_C1YA75/1-112 YTVELLPKVR VEILVDDEDA EDVVDVIVRA ARTGKIGDGK VWTQPVETVI +UniRef90_A8KX44/1-112 FHDESTSNIR LELVVADSDA PDVVNVIRRT AASTSSGAGK IWVLPVEGLA +UniRef90_C0EZB6/1-110 IDMNLLPQLQ VDIVVSTVPP ELVVEAAKKA LYTGEYGDGK IFLYDVENVV +UniRef90_Q11P32/1-112 KSIVLLSKVM IICVVSDENL EKCIDVIIET GSEGKVGDGK IFVYDVLDAI +UniRef90_A7B6Y7/1-112 VDILLHPKIK FEVVVSSEEW EQTISAIQKA AFTGEVGDGK IFSYEIRSAV +UniRef90_A7VSI5/1-111 LDIVLLPKIK LEIVVSKVPV QTV-DTARKV LYTGNIGDGK IFIYDVENVI +UniRef90_A6G036/1-110 YVIDFVPKIK IEVVVPAARS EEVIAAIREV AASDRIGDGK IFVTPVLEAV +UniRef90_C0ES36/1-115 VDMQMQPKIK FEIVVSSEEW EKTIEAIEKA AYTGEPGDGK IFTYEIRHAQ +UniRef90_B5IHX8/1-113 VEAKLLTKMQ ITSVVTDQAV DQVVQAILTA ARTGEIGDGK IVITPVENAI +UniRef90_B0MIE7/1-103 LNSNLLPKIK VESVMPEEVV EKVTKDIVNT VRTGEFGDGK IFISPVEEAI +UniRef90_B4S395/1-111 IAPNLRPKIK LEIAVNEEFV DVAIDTIVDS ARSGEIGDGK IFVTPLEQCV +UniRef90_P51254/1-112 YSIDIIDKIK IEIIVSDDKV NSITEIIIKT AKTGEIGDGK IFISDVEQVI +UniRef90_P71524/1-104 IYYDELPKTM LMLVVEDDAA ENVIELITKT AYTGSFGDGK IFVSPVDEAY +UniRef90_A8JI83/1-105 FGPNLVDKEK LDIVVSRAQV DAVVRLVAAS AYTGEIGDGK IFVHPVAEVV +UniRef90_B0CD03/1-107 AEIRLHRKLK VEVKVDEEMV APVVEKITFA ARTGQVGDGK IFVSPLQKVV +UniRef90_B1QY06/1-112 LITNVLPKIE VKMVIEDSKV EEVIEIISSI AKTGEVGDGK IFVIDICDCV +UniRef90_Q30VL0/1-106 TEVNLLKKVR IEVGVPADKA EDALAALQTG AHTGREGDGI IFVQDVARTV +UniRef90_A0T2Q5/1-113 MRMKYIPKRM ISIVVDDADV PFVVGIIMKV NRTGKPGDGK IFVLPVEEAI +UniRef90_B3QXW9/1-112 EGYELVSKRY LVVVVNDNML QPTIDAIISA NQTGKPGDGK IFVSTIEDAV +UniRef90_B6YRQ4/1-111 YDTSSIERIQ INLVVRDINV EKAIKAIEKS AHTGEVGDGR IFVSTIDNAY +UniRef90_B0MJN0/1-114 VDARLLPKMK VEIVVCKVPV EKVVEVAKNA LYTGKIGDGK IFVYDVENVI +UniRef90_C2C1T3/1-112 KENNVHERMK VEIVVSTVPV EAVLEVVKNT LRTGEPGDGK VFVYPLSDVI +UniRef90_C1VTA2/1-110 YVIDLHQKIK VECVVEPEDA DDVVEAIREG ANTGEKGDGK IFVLPVFDAV +UniRef90_A3XNG5/1-112 YSTSDIQRRY LSIVVNDDFE QAAVAAILDA AATGEVGDGK IFVSDVQDAY +UniRef90_P71525/1-111 -DMRYIPKTM LTLIVPDEDA SLVVEAIMKV NKSGQYGDGK IFVCPIEDII +UniRef90_Q46C91/1-112 RRMEYIPKRL FSIVTRNEDV DTIIETIMKV NQTGDIGDGR IFICPVDDAI +UniRef90_B7BWA8/1-112 VKHRLVAKRM IDMFVRDEDL QKLIDTVVEV NKTNHAGDGK IFVLPVNDAI +UniRef90_Q7UGU6/1-112 YGVSLLRKVQ LQIGVNEEFV QPTIDAIGRS GESGEIGDGK IFVLPMDDCV +UniRef90_A3HVG6/1-112 YEPTYIPRTK LEIVTVDELV EPVINCILTE GKTGEVGDGK IFVYDVLEAH +UniRef90_A0YMH7/1-112 HVIEFHPKMK LEIVVEDEVC EFVVEKLVEA AQTGQIGDGK IFIQSMEHII +UniRef90_Q46A23/1-112 YEANLLDKVK IEIAVKDEFL QTTVEAIERG SKDGYIGSGK IFVLPLENVM +UniRef90_B4VJP7/1-90 VLYDELPKAL LMVVVPDTEK EFVIRAILSS ARTGAEGDGK IFVSPVEEVY +UniRef90_B1QUW3/1-103 VHYDELPKEM LLIVVKDEDK DDVVRVIMKN SRTGEYGDGK IFISKVDTAY +UniRef90_A5N1U1/1-112 ESYRLISKRL IWILAKDEDV KKIADIIIDI NQTGHPGDGK IFVTKVTDVV +UniRef90_A9D1T1/1-65 YMVDFLPKVK IELVIQDELL DRAIEVIVDT ARTGKIGDGK IFVTEIERVI +UniRef90_A6LUZ0/1-104 VYYDELPKEM LLIAVKDEDK DDVIKVIIRN SRTGEFGDGK IFVAPIEEVY +UniRef90_A6LUZ1/1-112 EVPRLIPKRF ITLVVKDDEV KTVVDTVISV NSTGTPGDGK IFVLPVEEVY +UniRef90_B8GEW5/1-112 QEVRFFPRRL FTILAHDEDV PRIVEAITKV NITEKVGDGI ILVLPVDDAV +UniRef90_C1FI34/1-109 FDANLVEKVV VEIVVVREQC QEVVDVIVDA AQTGEIGDGK IFLSPVHDIV +UniRef90_C1TA34/1-112 GGTRLIPKRL LTILARDEDV KKIVDTVIKV NQEGNKGDGR IFIAPVIDAY +UniRef90_C1T440/1-112 KGIELYPKRM LTVVVTDDLV PEVVKVITDT NKTGQPGDGK IFVLPMIDAV +UniRef90_A9A2H4/1-100 LVGDFFSRVL IVCVVDDPKL DEILDAIAGA ACTGTKGDGK VYVSDICDAL +UniRef90_Q97ME3/1-112 ELSELISKRL IIILAKDEDV KEIVDEIIEV NRTGNPGDGK IFVINIADAM + + + 101 150 +QUERY/1-116 RIRTGEKNAD AISAWS +UniRef90_C0EK60/1-112 RIRTGERSEA AL---- +UniRef90_Q21P81/1-112 RIRTGETGPE AV---- +UniRef90_Q47GI8/1-112 RIRTGETDEA AV---- +UniRef90_B9ZJ79/1-112 RIRTGEEGSE AL---- +UniRef90_B5FAN6/1-112 RIRTGETDTE AL---- +UniRef90_B5ZIL8/1-112 RIRTGEHGEE AI---- +UniRef90_B4RVM6/1-112 RIRTGEQNED AI---- +UniRef90_B2FHB8/1-112 RIRTGEIGAD AL---- +UniRef90_P21193/1-112 RIRTGEKGGD AI---- +UniRef90_B5JS45/1-112 RIRTGEEDES AI---- +UniRef90_Q07UM0/1-112 RIRTGETNAD AL---- +UniRef90_Q2RVB4/1-112 RIRTGERGEE AL---- +UniRef90_A9IPV3/1-112 RIRTGESGEA AL---- +UniRef90_A4TZT2/1-112 RIRTGEADTE AL---- +UniRef90_B3DVA4/1-110 RIRTEEKGEN AI---- +UniRef90_C1STD4/1-112 RIRTGESGAE AL---- +UniRef90_A7HGG9/1-112 RVRTGERGED AL---- +UniRef90_A9BCF1/1-112 RIRTGELDGS AL---- +UniRef90_B4U911/1-112 RIRTGERGES AI---- +UniRef90_B1ZSX2/1-112 RIRTDERGEA AL---- +UniRef90_Q7X1L4/1-112 RIRTGETGDA AL---- +UniRef90_Q1NW36/1-112 RIRTGELDQD AI---- +UniRef90_C0GRX0/1-112 RIRTGESGDE AI---- +UniRef90_B8DJ84/1-112 RIRTGEEGTD AI---- +UniRef90_Q6ARG9/1-112 RVRTGEQGRE AI---- +UniRef90_C1W154/1-112 RVRTGEEGPS AL---- +UniRef90_C1UII8/1-112 RVRTGERGAD AL---- +UniRef90_UPI000/1-118 GKKGVFRGTS FEIQLV +UniRef90_C1T022/1-113 RIRTQETGPA AMG--- +UniRef90_Q46G48/1-112 RIRTNETGPE AL---- +UniRef90_A2RJQ2/1-112 RIRTSEEDAQ AL---- +UniRef90_Q8KF33/1-112 RIRTGESGDE SL---- +UniRef90_B1HTS9/1-112 RIRTKEVGSI AV---- +UniRef90_A2SPS9/1-106 WVRTDE---- ------ +UniRef90_C0EAH3/1-111 KVRTGEEGCA ALQ--- +UniRef90_A7I8Z1/1-104 RIRTGD---- ------ +UniRef90_Q3AFZ0/1-114 RIRTGERGTA AITS-- +UniRef90_A7I508/1-106 RIRTGE---- ------ +UniRef90_P51604/1-112 RVRTKESGED AI---- +UniRef90_B0NXT3/1-112 KIRTGERDVD ALQD-- +UniRef90_A8YG01/1-96 RIRTGEKDLQ AI---- +UniRef90_C0BMJ9/1-112 RIRTRENGKA GIN--- +UniRef90_Q466Y2/1-112 RIRTGERNGD AL---- +UniRef90_O26760/1-112 RIRTGESGKK AV---- +UniRef90_A0LYN2/1-111 RIRTKEKGGE SL---- +UniRef90_C1YA75/1-112 RVRTGERGPE AL---- +UniRef90_A8KX44/1-112 RIRTGERGAD AL---- +UniRef90_C0EZB6/1-110 RIRTNETGIA AL---- +UniRef90_Q11P32/1-112 RMRTRTRGDD AI---- +UniRef90_A7B6Y7/1-112 KIRTKETGYN AVQS-- +UniRef90_A7VSI5/1-111 KVRTGAEGYY ALQD-- +UniRef90_A6G036/1-110 RIRTDERGES AL---- +UniRef90_C0ES36/1-115 KIRTKETGYD AIQAT- +UniRef90_B5IHX8/1-113 RIRTGESGDS TLA--- +UniRef90_B0MIE7/1-103 RIRTGETGKD AL---- +UniRef90_B4S395/1-111 RIRTNERGGS AI---- +UniRef90_P51254/1-112 RIRTNDLNSA AL---- +UniRef90_P71524/1-104 TVRTRSCG-- ------ +UniRef90_A8JI83/1-105 RIRTAETG-- ------ +UniRef90_B0CD03/1-107 QVRTGEE--- ------ +UniRef90_B1QY06/1-112 RIRTGERGNE AL---- +UniRef90_Q30VL0/1-106 RVRTGE---- ------ +UniRef90_A0T2Q5/1-113 RIRTGEFGVE AIG--- +UniRef90_B3QXW9/1-112 RVRTGETGSA IL---- +UniRef90_B6YRQ4/1-111 SIRTGEQGDE TL---- +UniRef90_B0MJN0/1-114 KVRTGEEAYE ALQD-- +UniRef90_C2C1T3/1-112 KISTGEHGVA ALQD-- +UniRef90_C1VTA2/1-110 QVRTGDRGTD AI---- +UniRef90_A3XNG5/1-112 RIRTGKKGPD TLN--- +UniRef90_P71525/1-111 TVRTSERGEA AI---- +UniRef90_Q46C91/1-112 RVRTDEHGDN AL---- +UniRef90_B7BWA8/1-112 RVRTGEKGIE AI---- +UniRef90_Q7UGU6/1-112 RIRTGERGGE AI---- +UniRef90_A3HVG6/1-112 RIRNNDQGEQ AL---- +UniRef90_A0YMH7/1-112 RTRTGESDLE AL---- +UniRef90_Q46A23/1-112 RIRTKETGND AL---- +UniRef90_B4VJP7/1-90 TISSGKTDSS ------ +UniRef90_B1QUW3/1-103 TISTGKE--- ------ +UniRef90_A5N1U1/1-112 RIRTGETQDE AV---- +UniRef90_A9D1T1/1-65 RIRTGEENEE AV---- +UniRef90_A6LUZ0/1-104 TVSSGKSG-- ------ +UniRef90_A6LUZ1/1-112 RVRDGQIGEE AI---- +UniRef90_B8GEW5/1-112 RVRTGESGDA AI---- +UniRef90_C1FI34/1-109 RIRTGEVGAA A----- +UniRef90_C1TA34/1-112 RVRTAEKGEA AV---- +UniRef90_C1T440/1-112 RVRTGEKGAK SI---- +UniRef90_A9A2H4/1-100 DICTKKRG-- ------ +UniRef90_Q97ME3/1-112 RIRTEETGDM AI---- + + diff --git a/binaries/src/jpred/tests/d1b3aa_.fas b/binaries/src/jpred/tests/d1b3aa_.fas new file mode 100644 index 0000000..6e761aa --- /dev/null +++ b/binaries/src/jpred/tests/d1b3aa_.fas @@ -0,0 +1,2 @@ +>d1b3aa_ d.9.1.1 (A:) RANTES (regulated upon activation, normal T-cell expressed and secreted) {Human (Homo sapiens) [TaxId: 9606]} +PYSSDTTPCCFAYIARPLPRAHIKEYFYTSGKCSNPAVVFVTRKNRQVCANPEKKWVREYINSLEMS diff --git a/binaries/src/jpred/tests/res_d16vpa_.align b/binaries/src/jpred/tests/res_d16vpa_.align deleted file mode 100644 index e846252..0000000 --- a/binaries/src/jpred/tests/res_d16vpa_.align +++ /dev/null @@ -1,78 +0,0 @@ ->QUERY -SRMPSPPMPVPPAALFNRLLDDLGFSAGPALCTMLDTWNEDLFSALPTNADLYRECKFLSTLPSDVVEWGDA -YVPERTQIDIRAHGDVAFPTLPATRDGLGLYYEALSRFFHAELRAREESYRTVLANFCSALYRYLRASVRQL -HRQAHMRGRDRDLGEMLRATIADRYYRETARLARVLFLHLYLFLTREILWAAYAEQMMRPDLFDCLCCDLES -WRQLAGLFQPFMFVNGALTVRGVPIEARRLRELNHIREHLNLPLVRSAATEEPGAPLTTPPTLHGNQARASG -YFMVLIRAKLDSYSSFTTSPSEAVMREHAYSRAPTKNNYGSTIEGLLDLPDDDAPEEAGLAAPRLSFL ->UniRef90_Q00028 ------PPKATSPTALYQRLQAELGFPEGQAMLFAMEKWNEDMFSAIPVHVDLYTEIALLSTSVNEVVKAGLD -SLPIPTEVDLNAHGSEPFPEVPALEDELETYVISAQRFYLSELRAREEHYSRLLRGYCVALLHYLYGSAKRQ -LRGA---GSDSALMHKFKQVVRDRYYRETANLARLLYLHLYISVTREVSWRLHASQVVNQGIFVSLHYTWPQ -RRKFECLFHPVLFNHGVVILENDPLEFNDLQRINYRRRELGLPLIRAGLIEEENLPLESEPTFSGKLPRTIG -FLTHQIRTKMEAYSNAHPSTPLFPLAEHSYSRIDGRLSYGTTAEAMMDPPSPSA-------------- ->UniRef90_Q8B635 ------PIKASSPSSLIKNLLDELNFPEGPSLLSSMEKWNEDLFSCIPRFLEIYIENSILSTSVDEVIKNLDN -SLNYDDVIDFQVHGPETFPKTPLLEEELENYVTSVQKYFLSELKAREVTYSFLLTKYCKALLLYLRYNTKSS -IKG------NKDINQKFKQNVRERYYREVANIARLLYLHLYLSVTREVSWKLHADQVLLQSVFVSLSYSWSH -RRQFECIFHPILFNHGIVNLENNPLTFKELQKINYRRHILGLPLIRAGLVEEDNQPLMIPPEFSSKLPRTIG -FLTQQIRAKMEAYSDNHPVTPKFPRIEHSYAKPIDPINYGTTIEAMMDPPSPSA-------------- ->UniRef90_Q9E205 ------PPRVASPAVLYQQLINDLHFSEGPRIIALLETCNEDIFSCFPLNEDLYTDTIVFSTNPSDIIELETS -ETPE--PINLITKG-CDLPSLPSTYTELPMYVENVQNTFFTELRVREKAYLRLLILYCKSLLRHLQGISRRS -SVGARSQDCEHKYITQFKQSIRLRYYREVAKLARLLYLHLYITVTRQFSWRLFAQQSKYPDVFAAMKFMWLE -NRQFTCAFHPILCNHGIVLLEGKPLSSQRLREVNYRRRQLGLPLVRCALIEEKGVPLVQRPEFSAHMPRSLG -FLTHHIKAKLDVYSSKHSQEPGNVRVDHPYARNVNNINYGSSVEAMIVSPPSPS-------------- ->UniRef90_Q88530 ---LPSPE-AASPNLLYDRLILELDFAEGPSLLAKLERVNVDLFSCLPLNSHLYKHAKILSTCPREVLDAVYE -NTWQYTALNLNEHGKSSIPPVPASKDDLPAYVTAVQEFYLEELEAREQIYAKLFFGYCRALIMHIIKSV--L -NESRGVRVSDDYVQNKARWYISNNYYRDAVRIAKLLYLHLYLSTTEIVSQRLEAMQTSLQDLFVYLRCEWGQ -GRQFWCIFQPMIYNHGVPMIEGRALTSLELGSSNYIRSELGLPLIRCELLEELESPVVFPPTFTATAPRSSG -YLFHNIRAKMELYSNIHPSPQLSGLSDHTYVRTHVPVNYGTTVEVLLDASDPDS-------------- ->UniRef90_B4XS08 -------------------------FPEASTILSTFELMNMDLFSCLPRNEDLYRNAALLSGSVTEVIEA--S -EIPIDGEIDLNAHGSKQLPIPPSNEWEIPNYVEAVQQFFLSELRAREESYLKLFLGYCRAIVNYIKSAATRG -VRGCRIMDRKSEANKRMRRMIADRYYREAARLAKVLYLHLYLSVAREISSRLCATQMQVQNVFVYMRYEWQQ -YRQFTCLFHPIMFNHGVVLLNGEPLQAQKLREVNYIRFKLGLPVIRCGLVEEHDKPLVEEPRFYGNLPRSSG -FLTELIRSKMEAYSELRPTSPSSISNDHTYAKQLDKVNFGSTREAILDTIDTEGP------------- ->UniRef90_P09265 ----PSPPWVASPKILYQQLIRDLDFSEGPRLLSCLETWNEDLFSCFPINEDLYSDMMVLSPDPDDVI----S -TVSTKDHVNLTTRGSVRLPSPPKQPTGLPAYVQEVQDSFTVELRAREEAYTKLLVTYCKSIIRYLQGTAKRT -TIGLNIQNPDQKAYTQLRQSILLRYYREVASLARLLYLHLYLTVTREFSWRLYASQSAHPDVFAALKFTWTE -RRQFTCAFHPVLCNHGIVLLEGKPLTASALREINYRRRELGLPLVRCGLVEENKSPLVQQPSFSVHLPRSVG -FLTHHIKRKLDAYAVKHPQEPRHVRADHPYAKVVENRNYGSSIEAMILAP--PSPSE----------- ->UniRef90_Q2QBC8 -------------AALYNRLLEDLGFGDGPALCTILDSWNEDLFSGLPANPDLYRECRFLSTLPGDVVVWGDA -HAPDRGPIDIRAHGSAPFPSLPARREGLPAYCEALTRFFHSELRAREESYRRVLANFCSALYRYLRASTRQL -HRQAALKGRPRDLQEMLRAAVAERYYRETARLARVLFLHLYLFLVREILWAVYAEQVMRQDLFEGLRCDLEQ -ARQLSCLFQPLLFVHGALSVGGEPVSPARLRELNHVRERLNLPLIRSAATEEPGAALTAAPALQTQRARSSG -YFMTLIRVKLDAYSEWSAGSEGAVLREHAYSRRRERTNYGSSIEGLLEL------------------- ->UniRef90_Q90603 ----------------YTRLLHELDFVEGPSILARLEKINVDLFSCFPHNKHLYEHAKILSVSPSEVLEELSK -NTWTYTALNLNEHGEVALPMPPTTKADLPSYVDDIQNFYLGELEAREKSYATMFYGYCRALAEYIRQSAIKD -LRDA--RVEDKNIGACSKARQYIAERYYREAFANVLYVHLYLSTTRDVSQRLEASQMGRQNIFVYLKCEWLQ -ERHFHCLFQPVIFNHGVVIVEGRVLTAPELRAQNYIRSEFGLPLIRCKLVEEPDMPLISPPPFSGDAPRASV -YLLQCIRSKLEVYSSHPPNPQLHVHKEHVHQKLESPPNYGTTVEALLMDSSD---------------- ->UniRef90_O89246 ---------------------HELDFTEGPSLLSRLEKLNVDLFSCFPINGHLYEHATLLSVSPSEVLDAASE -EKWAYTAINLNEHCGMEVPRPPLTKDGLPVYVTEIQKFFSMELEAREKSYVTLLCGYCRALACYLRQGANEP -SRCDMCVGGS----ETPRRSIAGAYYREAARFARLLYMHLYLSVTRDVSRRLEASQRKRQNLFAHLRCDWHQ -LRHFQCLFQPVIFNHGVVIVEGRALTAAELRTQNYVRSELGLPVMRCELVEERGMPLTAPPAFLANAPRASA -YLFQCIKSKLEVYSLMHPPRPRSSARGESGRAGKAGPSHGTIVKAMLRDSTHPGPAIADIAAAR---- ->UniRef90_Q5PP87 -----------SPDALYQRLISDLAFDEGPALLGAMERWNEDLFSCLPGNEDLYARLVMLSASADEVAAQVRA -PTADAS-VDLGVPGAEPMPRVPAVEEELPAYVAAVERFFVSTLRAREERYARLLDAYCRAVLRYLHAQARRD --------------EGKLRQLVRGRYYRDVARLAPWLFLHLYVATARELSWRLHADQVVAQDVFMSLRYEWDQ -ARQLTCLFHPVLFNHGVVLLSGAPVPAAQLRAVNHRRRELGLPLVRAGLIEEDGADLVEEPPFSAALPRAAG -YLSHQVRIKMEAYS--------REYRDHTYCRPPSPVSYG---------------------------- ->UniRef90_Q65819 -----------------ERMQAELGFPDGPALLRAMERWNEDLFSCLPTNADLYADAALLSADADAVVGAMYL -AVPDAERLDLNAHANQPLPAPPASEEGLPEYVAGVQAHFLAELRAREERYAGLFLGYCRALLQHLRA----T -AARGRGAAGAGAQADRLRQLVAARYYREASRLARLAFAHMYVATAREVSWRLHSQQSQAQGVFVSLYYAWPQ -RRQFTCLFHPVLFNHGVVALEDGFLDAAELRRLNYRRRELGLPLVRAGLVEVEVGPLVEEPPFSGSLPRALG -FLNYQVRAKMGAPAE--AGGRLAPEREHSYARPRGAINYGTTPEAMLRPPSPS--------------- ->UniRef90_O56869 --RNPGPPALVSASFLAKNALTELQFADWDKIQHVLKTINIDIFSCVPVGENGLCNMDWFSLDTEKIWTLMDS -GTPNVSPNLLITPGPP--PECIKTPEEAPAYFEAISNYFESVLAAREAEYAKLLAEYAKSLAKYIRHKSQKV -GR--GLRALELDTEEAKKRLMKSEYYKGIEKLLIIFLVHLVLNACRDVARIIWVQQRDSSSVLQKVTYRWES --QQLHCIFQPLLVSPGPVFLDNDPLPLQTLQHVNYVRYLLGVPVLRFSMIEESPSAQYIP----YDKTAPSA -YDVLATIAR----TCLTSSGCSRASHDHTYARDNEKPNYSSSRIVLLADSALDTP------------- diff --git a/binaries/src/jpred/tests/res_d16vpa_.concise b/binaries/src/jpred/tests/res_d16vpa_.concise deleted file mode 100644 index 38a9914..0000000 --- a/binaries/src/jpred/tests/res_d16vpa_.concise +++ /dev/null @@ -1,25 +0,0 @@ -align1;QUERY:S,R,M,P,S,P,P,M,P,V,P,P,A,A,L,F,N,R,L,L,D,D,L,G,F,S,A,G,P,A,L,C,T,M,L,D,T,W,N,E,D,L,F,S,A,L,P,T,N,A,D,L,Y,R,E,C,K,F,L,S,T,L,P,S,D,V,V,E,W,G,D,A,Y,V,P,E,R,T,Q,I,D,I,R,A,H,G,D,V,A,F,P,T,L,P,A,T,R,D,G,L,G,L,Y,Y,E,A,L,S,R,F,F,H,A,E,L,R,A,R,E,E,S,Y,R,T,V,L,A,N,F,C,S,A,L,Y,R,Y,L,R,A,S,V,R,Q,L,H,R,Q,A,H,M,R,G,R,D,R,D,L,G,E,M,L,R,A,T,I,A,D,R,Y,Y,R,E,T,A,R,L,A,R,V,L,F,L,H,L,Y,L,F,L,T,R,E,I,L,W,A,A,Y,A,E,Q,M,M,R,P,D,L,F,D,C,L,C,C,D,L,E,S,W,R,Q,L,A,G,L,F,Q,P,F,M,F,V,N,G,A,L,T,V,R,G,V,P,I,E,A,R,R,L,R,E,L,N,H,I,R,E,H,L,N,L,P,L,V,R,S,A,A,T,E,E,P,G,A,P,L,T,T,P,P,T,L,H,G,N,Q,A,R,A,S,G,Y,F,M,V,L,I,R,A,K,L,D,S,Y,S,S,F,T,T,S,P,S,E,A,V,M,R,E,H,A,Y,S,R,A,P,T,K,N,N,Y,G,S,T,I,E,G,L,L,D,L,P,D,D,D,A,P,E,E,A,G,L,A,A,P,R,L,S,F,L, -align2;UniRef90_Q00028:-,-,-,-,-,P,P,K,A,T,S,P,T,A,L,Y,Q,R,L,Q,A,E,L,G,F,P,E,G,Q,A,M,L,F,A,M,E,K,W,N,E,D,M,F,S,A,I,P,V,H,V,D,L,Y,T,E,I,A,L,L,S,T,S,V,N,E,V,V,K,A,G,L,D,S,L,P,I,P,T,E,V,D,L,N,A,H,G,S,E,P,F,P,E,V,P,A,L,E,D,E,L,E,T,Y,V,I,S,A,Q,R,F,Y,L,S,E,L,R,A,R,E,E,H,Y,S,R,L,L,R,G,Y,C,V,A,L,L,H,Y,L,Y,G,S,A,K,R,Q,L,R,G,A,-,-,-,G,S,D,S,A,L,M,H,K,F,K,Q,V,V,R,D,R,Y,Y,R,E,T,A,N,L,A,R,L,L,Y,L,H,L,Y,I,S,V,T,R,E,V,S,W,R,L,H,A,S,Q,V,V,N,Q,G,I,F,V,S,L,H,Y,T,W,P,Q,R,R,K,F,E,C,L,F,H,P,V,L,F,N,H,G,V,V,I,L,E,N,D,P,L,E,F,N,D,L,Q,R,I,N,Y,R,R,R,E,L,G,L,P,L,I,R,A,G,L,I,E,E,E,N,L,P,L,E,S,E,P,T,F,S,G,K,L,P,R,T,I,G,F,L,T,H,Q,I,R,T,K,M,E,A,Y,S,N,A,H,P,S,T,P,L,F,P,L,A,E,H,S,Y,S,R,I,D,G,R,L,S,Y,G,T,T,A,E,A,M,M,D,P,P,S,P,S,A,-,-,-,-,-,-,-,-,-,-,-,-,-,-, -align3;UniRef90_Q8B635:-,-,-,-,-,P,I,K,A,S,S,P,S,S,L,I,K,N,L,L,D,E,L,N,F,P,E,G,P,S,L,L,S,S,M,E,K,W,N,E,D,L,F,S,C,I,P,R,F,L,E,I,Y,I,E,N,S,I,L,S,T,S,V,D,E,V,I,K,N,L,D,N,S,L,N,Y,D,D,V,I,D,F,Q,V,H,G,P,E,T,F,P,K,T,P,L,L,E,E,E,L,E,N,Y,V,T,S,V,Q,K,Y,F,L,S,E,L,K,A,R,E,V,T,Y,S,F,L,L,T,K,Y,C,K,A,L,L,L,Y,L,R,Y,N,T,K,S,S,I,K,G,-,-,-,-,-,-,N,K,D,I,N,Q,K,F,K,Q,N,V,R,E,R,Y,Y,R,E,V,A,N,I,A,R,L,L,Y,L,H,L,Y,L,S,V,T,R,E,V,S,W,K,L,H,A,D,Q,V,L,L,Q,S,V,F,V,S,L,S,Y,S,W,S,H,R,R,Q,F,E,C,I,F,H,P,I,L,F,N,H,G,I,V,N,L,E,N,N,P,L,T,F,K,E,L,Q,K,I,N,Y,R,R,H,I,L,G,L,P,L,I,R,A,G,L,V,E,E,D,N,Q,P,L,M,I,P,P,E,F,S,S,K,L,P,R,T,I,G,F,L,T,Q,Q,I,R,A,K,M,E,A,Y,S,D,N,H,P,V,T,P,K,F,P,R,I,E,H,S,Y,A,K,P,I,D,P,I,N,Y,G,T,T,I,E,A,M,M,D,P,P,S,P,S,A,-,-,-,-,-,-,-,-,-,-,-,-,-,-, -align4;UniRef90_Q9E205:-,-,-,-,-,P,P,R,V,A,S,P,A,V,L,Y,Q,Q,L,I,N,D,L,H,F,S,E,G,P,R,I,I,A,L,L,E,T,C,N,E,D,I,F,S,C,F,P,L,N,E,D,L,Y,T,D,T,I,V,F,S,T,N,P,S,D,I,I,E,L,E,T,S,E,T,P,E,-,-,P,I,N,L,I,T,K,G,-,C,D,L,P,S,L,P,S,T,Y,T,E,L,P,M,Y,V,E,N,V,Q,N,T,F,F,T,E,L,R,V,R,E,K,A,Y,L,R,L,L,I,L,Y,C,K,S,L,L,R,H,L,Q,G,I,S,R,R,S,S,V,G,A,R,S,Q,D,C,E,H,K,Y,I,T,Q,F,K,Q,S,I,R,L,R,Y,Y,R,E,V,A,K,L,A,R,L,L,Y,L,H,L,Y,I,T,V,T,R,Q,F,S,W,R,L,F,A,Q,Q,S,K,Y,P,D,V,F,A,A,M,K,F,M,W,L,E,N,R,Q,F,T,C,A,F,H,P,I,L,C,N,H,G,I,V,L,L,E,G,K,P,L,S,S,Q,R,L,R,E,V,N,Y,R,R,R,Q,L,G,L,P,L,V,R,C,A,L,I,E,E,K,G,V,P,L,V,Q,R,P,E,F,S,A,H,M,P,R,S,L,G,F,L,T,H,H,I,K,A,K,L,D,V,Y,S,S,K,H,S,Q,E,P,G,N,V,R,V,D,H,P,Y,A,R,N,V,N,N,I,N,Y,G,S,S,V,E,A,M,I,V,S,P,P,S,P,S,-,-,-,-,-,-,-,-,-,-,-,-,-,-, -align5;UniRef90_Q88530:-,-,L,P,S,P,E,-,A,A,S,P,N,L,L,Y,D,R,L,I,L,E,L,D,F,A,E,G,P,S,L,L,A,K,L,E,R,V,N,V,D,L,F,S,C,L,P,L,N,S,H,L,Y,K,H,A,K,I,L,S,T,C,P,R,E,V,L,D,A,V,Y,E,N,T,W,Q,Y,T,A,L,N,L,N,E,H,G,K,S,S,I,P,P,V,P,A,S,K,D,D,L,P,A,Y,V,T,A,V,Q,E,F,Y,L,E,E,L,E,A,R,E,Q,I,Y,A,K,L,F,F,G,Y,C,R,A,L,I,M,H,I,I,K,S,V,-,-,L,N,E,S,R,G,V,R,V,S,D,D,Y,V,Q,N,K,A,R,W,Y,I,S,N,N,Y,Y,R,D,A,V,R,I,A,K,L,L,Y,L,H,L,Y,L,S,T,T,E,I,V,S,Q,R,L,E,A,M,Q,T,S,L,Q,D,L,F,V,Y,L,R,C,E,W,G,Q,G,R,Q,F,W,C,I,F,Q,P,M,I,Y,N,H,G,V,P,M,I,E,G,R,A,L,T,S,L,E,L,G,S,S,N,Y,I,R,S,E,L,G,L,P,L,I,R,C,E,L,L,E,E,L,E,S,P,V,V,F,P,P,T,F,T,A,T,A,P,R,S,S,G,Y,L,F,H,N,I,R,A,K,M,E,L,Y,S,N,I,H,P,S,P,Q,L,S,G,L,S,D,H,T,Y,V,R,T,H,V,P,V,N,Y,G,T,T,V,E,V,L,L,D,A,S,D,P,D,S,-,-,-,-,-,-,-,-,-,-,-,-,-,-, -align6;UniRef90_B4XS08:-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,F,P,E,A,S,T,I,L,S,T,F,E,L,M,N,M,D,L,F,S,C,L,P,R,N,E,D,L,Y,R,N,A,A,L,L,S,G,S,V,T,E,V,I,E,A,-,-,S,E,I,P,I,D,G,E,I,D,L,N,A,H,G,S,K,Q,L,P,I,P,P,S,N,E,W,E,I,P,N,Y,V,E,A,V,Q,Q,F,F,L,S,E,L,R,A,R,E,E,S,Y,L,K,L,F,L,G,Y,C,R,A,I,V,N,Y,I,K,S,A,A,T,R,G,V,R,G,C,R,I,M,D,R,K,S,E,A,N,K,R,M,R,R,M,I,A,D,R,Y,Y,R,E,A,A,R,L,A,K,V,L,Y,L,H,L,Y,L,S,V,A,R,E,I,S,S,R,L,C,A,T,Q,M,Q,V,Q,N,V,F,V,Y,M,R,Y,E,W,Q,Q,Y,R,Q,F,T,C,L,F,H,P,I,M,F,N,H,G,V,V,L,L,N,G,E,P,L,Q,A,Q,K,L,R,E,V,N,Y,I,R,F,K,L,G,L,P,V,I,R,C,G,L,V,E,E,H,D,K,P,L,V,E,E,P,R,F,Y,G,N,L,P,R,S,S,G,F,L,T,E,L,I,R,S,K,M,E,A,Y,S,E,L,R,P,T,S,P,S,S,I,S,N,D,H,T,Y,A,K,Q,L,D,K,V,N,F,G,S,T,R,E,A,I,L,D,T,I,D,T,E,G,P,-,-,-,-,-,-,-,-,-,-,-,-,-, -align7;UniRef90_P09265:-,-,-,P,S,P,P,W,V,A,S,P,K,I,L,Y,Q,Q,L,I,R,D,L,D,F,S,E,G,P,R,L,L,S,C,L,E,T,W,N,E,D,L,F,S,C,F,P,I,N,E,D,L,Y,S,D,M,M,V,L,S,P,D,P,D,D,V,I,-,-,-,-,S,T,V,S,T,K,D,H,V,N,L,T,T,R,G,S,V,R,L,P,S,P,P,K,Q,P,T,G,L,P,A,Y,V,Q,E,V,Q,D,S,F,T,V,E,L,R,A,R,E,E,A,Y,T,K,L,L,V,T,Y,C,K,S,I,I,R,Y,L,Q,G,T,A,K,R,T,T,I,G,L,N,I,Q,N,P,D,Q,K,A,Y,T,Q,L,R,Q,S,I,L,L,R,Y,Y,R,E,V,A,S,L,A,R,L,L,Y,L,H,L,Y,L,T,V,T,R,E,F,S,W,R,L,Y,A,S,Q,S,A,H,P,D,V,F,A,A,L,K,F,T,W,T,E,R,R,Q,F,T,C,A,F,H,P,V,L,C,N,H,G,I,V,L,L,E,G,K,P,L,T,A,S,A,L,R,E,I,N,Y,R,R,R,E,L,G,L,P,L,V,R,C,G,L,V,E,E,N,K,S,P,L,V,Q,Q,P,S,F,S,V,H,L,P,R,S,V,G,F,L,T,H,H,I,K,R,K,L,D,A,Y,A,V,K,H,P,Q,E,P,R,H,V,R,A,D,H,P,Y,A,K,V,V,E,N,R,N,Y,G,S,S,I,E,A,M,I,L,A,P,-,-,P,S,P,S,E,-,-,-,-,-,-,-,-,-,-,-, -align8;UniRef90_Q2QBC8:-,-,-,-,-,-,-,-,-,-,-,-,A,A,L,Y,N,R,L,L,E,D,L,G,F,G,D,G,P,A,L,C,T,I,L,D,S,W,N,E,D,L,F,S,G,L,P,A,N,P,D,L,Y,R,E,C,R,F,L,S,T,L,P,G,D,V,V,V,W,G,D,A,H,A,P,D,R,G,P,I,D,I,R,A,H,G,S,A,P,F,P,S,L,P,A,R,R,E,G,L,P,A,Y,C,E,A,L,T,R,F,F,H,S,E,L,R,A,R,E,E,S,Y,R,R,V,L,A,N,F,C,S,A,L,Y,R,Y,L,R,A,S,T,R,Q,L,H,R,Q,A,A,L,K,G,R,P,R,D,L,Q,E,M,L,R,A,A,V,A,E,R,Y,Y,R,E,T,A,R,L,A,R,V,L,F,L,H,L,Y,L,F,L,V,R,E,I,L,W,A,V,Y,A,E,Q,V,M,R,Q,D,L,F,E,G,L,R,C,D,L,E,Q,A,R,Q,L,S,C,L,F,Q,P,L,L,F,V,H,G,A,L,S,V,G,G,E,P,V,S,P,A,R,L,R,E,L,N,H,V,R,E,R,L,N,L,P,L,I,R,S,A,A,T,E,E,P,G,A,A,L,T,A,A,P,A,L,Q,T,Q,R,A,R,S,S,G,Y,F,M,T,L,I,R,V,K,L,D,A,Y,S,E,W,S,A,G,S,E,G,A,V,L,R,E,H,A,Y,S,R,R,R,E,R,T,N,Y,G,S,S,I,E,G,L,L,E,L,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-, -align9;UniRef90_Q90603:-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,Y,T,R,L,L,H,E,L,D,F,V,E,G,P,S,I,L,A,R,L,E,K,I,N,V,D,L,F,S,C,F,P,H,N,K,H,L,Y,E,H,A,K,I,L,S,V,S,P,S,E,V,L,E,E,L,S,K,N,T,W,T,Y,T,A,L,N,L,N,E,H,G,E,V,A,L,P,M,P,P,T,T,K,A,D,L,P,S,Y,V,D,D,I,Q,N,F,Y,L,G,E,L,E,A,R,E,K,S,Y,A,T,M,F,Y,G,Y,C,R,A,L,A,E,Y,I,R,Q,S,A,I,K,D,L,R,D,A,-,-,R,V,E,D,K,N,I,G,A,C,S,K,A,R,Q,Y,I,A,E,R,Y,Y,R,E,A,F,A,N,V,L,Y,V,H,L,Y,L,S,T,T,R,D,V,S,Q,R,L,E,A,S,Q,M,G,R,Q,N,I,F,V,Y,L,K,C,E,W,L,Q,E,R,H,F,H,C,L,F,Q,P,V,I,F,N,H,G,V,V,I,V,E,G,R,V,L,T,A,P,E,L,R,A,Q,N,Y,I,R,S,E,F,G,L,P,L,I,R,C,K,L,V,E,E,P,D,M,P,L,I,S,P,P,P,F,S,G,D,A,P,R,A,S,V,Y,L,L,Q,C,I,R,S,K,L,E,V,Y,S,S,H,P,P,N,P,Q,L,H,V,H,K,E,H,V,H,Q,K,L,E,S,P,P,N,Y,G,T,T,V,E,A,L,L,M,D,S,S,D,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-, -align10;UniRef90_O89246:-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,E,L,D,F,T,E,G,P,S,L,L,S,R,L,E,K,L,N,V,D,L,F,S,C,F,P,I,N,G,H,L,Y,E,H,A,T,L,L,S,V,S,P,S,E,V,L,D,A,A,S,E,E,K,W,A,Y,T,A,I,N,L,N,E,H,C,G,M,E,V,P,R,P,P,L,T,K,D,G,L,P,V,Y,V,T,E,I,Q,K,F,F,S,M,E,L,E,A,R,E,K,S,Y,V,T,L,L,C,G,Y,C,R,A,L,A,C,Y,L,R,Q,G,A,N,E,P,S,R,C,D,M,C,V,G,G,S,-,-,-,-,E,T,P,R,R,S,I,A,G,A,Y,Y,R,E,A,A,R,F,A,R,L,L,Y,M,H,L,Y,L,S,V,T,R,D,V,S,R,R,L,E,A,S,Q,R,K,R,Q,N,L,F,A,H,L,R,C,D,W,H,Q,L,R,H,F,Q,C,L,F,Q,P,V,I,F,N,H,G,V,V,I,V,E,G,R,A,L,T,A,A,E,L,R,T,Q,N,Y,V,R,S,E,L,G,L,P,V,M,R,C,E,L,V,E,E,R,G,M,P,L,T,A,P,P,A,F,L,A,N,A,P,R,A,S,A,Y,L,F,Q,C,I,K,S,K,L,E,V,Y,S,L,M,H,P,P,R,P,R,S,S,A,R,G,E,S,G,R,A,G,K,A,G,P,S,H,G,T,I,V,K,A,M,L,R,D,S,T,H,P,G,P,A,I,A,D,I,A,A,A,R,-,-,-,-, -align11;UniRef90_Q5PP87:-,-,-,-,-,-,-,-,-,-,S,P,D,A,L,Y,Q,R,L,I,S,D,L,A,F,D,E,G,P,A,L,L,G,A,M,E,R,W,N,E,D,L,F,S,C,L,P,G,N,E,D,L,Y,A,R,L,V,M,L,S,A,S,A,D,E,V,A,A,Q,V,R,A,P,T,A,D,A,S,-,V,D,L,G,V,P,G,A,E,P,M,P,R,V,P,A,V,E,E,E,L,P,A,Y,V,A,A,V,E,R,F,F,V,S,T,L,R,A,R,E,E,R,Y,A,R,L,L,D,A,Y,C,R,A,V,L,R,Y,L,H,A,Q,A,R,R,D,-,-,-,-,-,-,-,-,-,-,-,-,-,E,G,K,L,R,Q,L,V,R,G,R,Y,Y,R,D,V,A,R,L,A,P,W,L,F,L,H,L,Y,V,A,T,A,R,E,L,S,W,R,L,H,A,D,Q,V,V,A,Q,D,V,F,M,S,L,R,Y,E,W,D,Q,A,R,Q,L,T,C,L,F,H,P,V,L,F,N,H,G,V,V,L,L,S,G,A,P,V,P,A,A,Q,L,R,A,V,N,H,R,R,R,E,L,G,L,P,L,V,R,A,G,L,I,E,E,D,G,A,D,L,V,E,E,P,P,F,S,A,A,L,P,R,A,A,G,Y,L,S,H,Q,V,R,I,K,M,E,A,Y,S,-,-,-,-,-,-,-,-,R,E,Y,R,D,H,T,Y,C,R,P,P,S,P,V,S,Y,G,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-, -align12;UniRef90_Q65819:-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,E,R,M,Q,A,E,L,G,F,P,D,G,P,A,L,L,R,A,M,E,R,W,N,E,D,L,F,S,C,L,P,T,N,A,D,L,Y,A,D,A,A,L,L,S,A,D,A,D,A,V,V,G,A,M,Y,L,A,V,P,D,A,E,R,L,D,L,N,A,H,A,N,Q,P,L,P,A,P,P,A,S,E,E,G,L,P,E,Y,V,A,G,V,Q,A,H,F,L,A,E,L,R,A,R,E,E,R,Y,A,G,L,F,L,G,Y,C,R,A,L,L,Q,H,L,R,A,-,-,-,-,T,A,A,R,G,R,G,A,A,G,A,G,A,Q,A,D,R,L,R,Q,L,V,A,A,R,Y,Y,R,E,A,S,R,L,A,R,L,A,F,A,H,M,Y,V,A,T,A,R,E,V,S,W,R,L,H,S,Q,Q,S,Q,A,Q,G,V,F,V,S,L,Y,Y,A,W,P,Q,R,R,Q,F,T,C,L,F,H,P,V,L,F,N,H,G,V,V,A,L,E,D,G,F,L,D,A,A,E,L,R,R,L,N,Y,R,R,R,E,L,G,L,P,L,V,R,A,G,L,V,E,V,E,V,G,P,L,V,E,E,P,P,F,S,G,S,L,P,R,A,L,G,F,L,N,Y,Q,V,R,A,K,M,G,A,P,A,E,-,-,A,G,G,R,L,A,P,E,R,E,H,S,Y,A,R,P,R,G,A,I,N,Y,G,T,T,P,E,A,M,L,R,P,P,S,P,S,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-, -align13;UniRef90_O56869:-,R,N,P,G,P,P,A,L,V,S,A,S,F,L,A,K,N,A,L,T,E,L,Q,F,A,D,W,D,K,I,Q,H,V,L,K,T,I,N,I,D,I,F,S,C,V,P,V,G,E,N,G,L,C,N,M,D,W,F,S,L,D,T,E,K,I,W,T,L,M,D,S,G,T,P,N,V,S,P,N,L,L,I,T,P,G,P,P,-,-,P,E,C,I,K,T,P,E,E,A,P,A,Y,F,E,A,I,S,N,Y,F,E,S,V,L,A,A,R,E,A,E,Y,A,K,L,L,A,E,Y,A,K,S,L,A,K,Y,I,R,H,K,S,Q,K,V,G,R,-,-,G,L,R,A,L,E,L,D,T,E,E,A,K,K,R,L,M,K,S,E,Y,Y,K,G,I,E,K,L,L,I,I,F,L,V,H,L,V,L,N,A,C,R,D,V,A,R,I,I,W,V,Q,Q,R,D,S,S,S,V,L,Q,K,V,T,Y,R,W,E,S,-,Q,Q,L,H,C,I,F,Q,P,L,L,V,S,P,G,P,V,F,L,D,N,D,P,L,P,L,Q,T,L,Q,H,V,N,Y,V,R,Y,L,L,G,V,P,V,L,R,F,S,M,I,E,E,S,P,S,A,Q,Y,I,P,-,-,-,-,Y,D,K,T,A,P,S,A,Y,D,V,L,A,T,I,A,R,-,-,-,-,T,C,L,T,S,S,G,C,S,R,A,S,H,D,H,T,Y,A,R,D,N,E,K,P,N,Y,S,S,S,R,I,V,L,L,A,D,S,A,L,D,T,P,-,-,-,-,-,-,-,-,-,-,-,-,-, - -jnetpred:-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,E,E,-,-,-,-,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,E,E,E,E,E,E,E,-,-,-,H,-,H,H,E,E,-,-,-,-,E,E,-,-,-,-,E,E,E,E,-,-,-,-,-,-,-,-,H,H,H,H,H,-,-,H,H,H,-,-,-,-,-,E,E,E,E,E,-,-,-,-,-,-,-,-,-,E,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-, -JNETCONF:9,9,8,8,8,8,8,7,7,6,3,6,8,8,9,9,9,9,8,7,4,4,7,8,8,8,7,4,6,8,8,9,9,9,9,9,8,5,4,2,3,2,2,2,3,2,3,5,6,6,5,1,0,1,2,2,2,4,0,5,7,6,1,6,8,8,8,7,6,3,2,3,6,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,6,4,1,0,2,3,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,8,7,3,2,1,4,1,1,1,5,7,7,7,7,5,1,7,8,9,9,9,9,9,9,9,9,9,8,5,4,6,8,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,8,6,1,1,1,4,4,5,5,2,1,3,5,4,5,6,4,4,6,3,0,1,1,1,1,1,1,3,4,5,1,1,2,5,6,4,5,7,7,5,3,6,8,7,7,6,5,4,1,0,0,1,1,1,0,4,3,2,1,0,5,7,5,1,1,1,1,1,0,0,1,7,8,7,7,5,2,1,0,3,6,7,6,5,6,7,7,6,2,1,2,6,6,8,9,9,9,9,8,8,7,5,1,0,2,4,6,7,7,7,7,7,6,7,7,7,7,7,7,6,4,1,4,6,7,7,7,7,7,7,7,6,5,1,0,3,3,3,2,1,6,7,7,7,7,6,5,4,4,5,7,7,7,7,6,3,3,4,2,6, -JNETSOL25:-,-,-,-,-,-,-,-,B,-,B,B,-,B,B,B,-,-,B,B,-,-,B,-,B,-,-,B,-,-,B,B,-,B,B,-,-,B,-,B,B,B,B,B,B,B,B,B,B,-,-,B,B,B,B,B,-,B,B,B,B,B,B,-,-,B,B,-,B,B,-,-,-,B,B,-,-,-,B,B,B,B,-,B,-,B,-,-,-,B,-,-,B,B,-,-,-,-,-,B,-,-,B,B,-,-,B,-,-,B,B,-,-,-,B,-,B,B,B,-,-,B,B,-,B,B,B,-,B,B,B,B,B,B,-,B,B,-,-,-,B,-,-,-,B,-,-,B,-,B,-,-,-,-,-,-,B,-,-,B,B,-,B,B,B,-,-,-,B,B,-,B,B,B,-,B,B,B,B,B,B,B,B,B,B,B,B,B,B,B,B,B,B,B,B,B,B,B,-,B,-,-,-,-,-,B,B,B,B,B,-,B,-,B,-,-,-,-,-,B,-,B,B,B,B,B,B,B,B,B,B,B,B,B,B,B,-,-,-,B,B,-,B,-,-,B,-,-,B,-,B,B,B,-,-,B,-,B,B,B,B,B,B,-,B,B,-,-,-,-,-,-,B,B,-,-,B,-,B,-,B,-,B,B,B,B,B,B,B,B,B,B,B,B,B,B,B,B,-,B,B,B,-,B,-,-,-,-,-,-,-,-,B,-,-,B,B,B,B,B,-,-,-,-,B,B,B,B,B,B,B,B,B,B,B,-,B,B,-,-,-,B,B,-,-,B,-,B,B,B,-,-,B,-,-,-, -JNETSOL5:-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,B,-,-,B,-,-,-,-,-,-,-,-,B,-,-,B,B,-,-,B,-,-,-,-,-,-,B,B,-,B,B,-,-,-,-,-,-,B,-,-,B,-,B,B,-,-,-,-,-,-,B,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,B,-,-,B,-,-,-,-,-,-,-,B,-,-,-,-,-,-,B,-,-,B,B,-,-,B,B,-,B,B,B,-,-,B,-,-,-,B,-,-,-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,-,B,-,-,-,B,-,-,-,-,-,-,-,B,-,-,B,B,-,B,B,-,B,-,-,-,B,-,B,B,-,-,B,B,-,-,B,-,-,-,-,-,-,-,-,-,B,B,-,-,B,-,B,-,-,-,-,-,-,-,B,-,B,B,B,-,B,-,B,B,-,-,B,B,B,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,B,-,B,B,-,B,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,B,-,B,-,B,-,-,-,B,-,-,-,B,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,B,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-, 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diff --git a/binaries/src/jpred/tests/res_d16vpa_.profile b/binaries/src/jpred/tests/res_d16vpa_.profile deleted file mode 100644 index 8e097f6..0000000 --- a/binaries/src/jpred/tests/res_d16vpa_.profile +++ /dev/null @@ -1,365 +0,0 @@ - -Last position-specific scoring matrix computed, weighted observed percentages rounded down, information per position, and relative weight of gapless real matches to pseudocounts - A R N D C Q E G H I L K M F P S T W Y V A R N D C Q E G H I L K M F P S T W Y V - 1 S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -2 -2 -1 4 1 -3 -2 -2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.00 0.00 - 2 R -1 6 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.00 0.00 - 3 M -2 -2 -3 -4 -2 -2 -3 -4 -3 1 4 -2 5 0 -3 -2 -1 -2 -1 1 0 0 0 0 0 0 0 0 0 0 50 0 50 0 0 0 0 0 0 0 0.46 0.07 - 4 P -1 -3 -3 -2 -3 -2 -2 -3 -3 -3 -4 -2 -3 -4 8 -1 -2 -4 -4 -3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 2.20 0.13 - 5 S 1 -1 0 -1 -1 0 -1 -1 -1 -3 -3 -1 -2 -3 -1 5 1 -3 -2 -2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0.63 0.13 - 6 P -2 -3 -3 -2 -4 -2 -2 -3 -3 -4 -4 -2 -3 -5 8 -2 -2 -5 -4 -3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 2.29 0.21 - 7 P -2 -2 -2 -1 -4 -1 2 -3 -2 -4 -4 -1 -3 -5 8 -1 -2 -4 -4 -3 0 0 0 0 0 0 19 0 0 0 0 0 0 0 81 0 0 0 0 0 1.76 0.21 - 8 M 1 3 -2 -3 -3 0 -1 -2 -2 -2 -1 3 4 -2 -3 -1 -2 7 -1 -2 19 17 0 0 0 0 0 0 0 0 0 27 20 0 0 0 0 17 0 0 0.46 0.21 - 9 P 2 -2 -2 -2 -1 -2 -2 -2 -2 0 -1 -2 -1 -2 4 -1 -1 -3 -2 3 28 1 1 1 0 1 1 1 0 1 2 1 0 1 21 1 1 0 1 35 0.36 0.17 - 10 V 4 -2 -2 -3 -1 -2 -2 -1 -3 -1 -2 -2 -1 -3 -2 0 2 -3 -2 2 66 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 20 0.44 0.21 - 11 P 0 -2 0 -1 -2 -1 -1 -1 -2 -3 -3 -1 -2 -3 4 5 1 -4 -3 -3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 80 0 0 0 0 0.73 0.21 - 12 P -2 -3 -3 -2 -4 -2 -2 -3 -3 -4 -4 -2 -4 -5 9 -2 -2 -5 -4 -3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 2.35 0.27 - 13 A 3 -2 2 2 -2 -1 -1 1 -2 -3 -3 1 -2 -4 -2 1 1 -4 -3 -2 40 0 12 11 0 0 0 7 0 0 0 11 0 0 0 10 7 0 0 0 0.36 0.30 - 14 A 4 -3 -3 -3 -2 -2 -2 -2 -3 1 1 -2 -1 -2 -2 1 -1 -4 -3 1 56 0 0 0 0 0 0 0 0 11 12 0 0 0 0 10 0 0 0 11 0.40 0.30 - 15 L -3 -3 -5 -5 -2 -3 -4 -5 -4 1 6 -4 1 -1 -4 -4 -2 -3 -2 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0.95 0.36 - 16 F 1 -3 -3 -4 -3 -3 -3 -4 0 0 -2 -3 -2 4 -4 -2 -2 0 7 -2 15 0 0 0 0 0 0 0 0 7 0 0 0 15 0 0 0 0 62 0 0.98 0.39 - 17 N -2 0 3 1 -4 5 2 -3 -1 -4 -4 3 -2 -4 -3 -1 1 -4 -3 -4 0 0 20 8 0 32 12 0 0 0 0 21 0 0 0 0 8 0 0 0 0.61 0.41 - 18 R -3 6 3 -2 -5 3 -1 -3 -1 -4 -4 1 -3 -4 -3 -1 -2 -4 -3 -4 0 64 21 0 0 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.97 0.41 - 19 L 1 -3 -4 -5 -2 -3 -4 -4 -4 0 5 -3 4 -1 -4 -3 -2 -3 -2 0 14 0 0 0 0 0 0 0 0 0 74 0 12 0 0 0 0 0 0 0 0.72 0.41 - 20 L -3 -3 -4 -4 -3 3 -2 -5 -3 4 4 -2 0 -1 -4 -3 -2 -3 -2 0 0 0 0 0 0 21 0 0 0 30 49 0 0 0 0 0 0 0 0 0 0.59 0.41 - 21 D 1 1 1 3 -3 -1 0 0 3 -3 -1 -1 -2 -4 -3 1 2 -4 -3 -3 17 8 7 20 0 0 6 5 8 0 8 0 0 0 0 7 14 0 0 0 0.26 0.41 - 22 D -2 -2 -1 5 -5 0 6 -3 -2 -5 -5 -1 -4 -5 -3 -1 -2 -5 -4 -4 0 0 0 39 0 0 61 0 0 0 0 0 0 0 0 0 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0.88079708 0.50000000 0.04742587 0.04742587 0.26894142 0.11920292 0.26894142 0.73105858 diff --git a/binaries/src/jpred/tests/res_d16vpa_.res b/binaries/src/jpred/tests/res_d16vpa_.res deleted file mode 100644 index 55507ce..0000000 --- a/binaries/src/jpred/tests/res_d16vpa_.res +++ /dev/null @@ -1,114 +0,0 @@ ->jnetpred ------------HHHHHHHHHH-------HHHHHHHHHHHHHHH-------------EE----HHHHHHHHH- -------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH -H--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------EEEEEEE--- -H-HHEE----EE----EEEE--------HHHHH--HHH-----EEEEE---------E----------HHHH -HHHHHHHHHHHH------------------------------HHHHH--------------------- ->JNETSOL25 ---------B-BB-BBB--BB--B-B--B--BB-BB--B-BBBBBBBBBB--BBBBB-BBBBBB--BB-BB-- --BB---BBBB-B-B---B--BB-----B--BB--B--BB---B-BBB--BB-BBB-BBBBBB-BB---B--- -B--B-B------B--BB-BBB---BB-BBB-BBBBBBBBBBBBBBBBBBBBBBB-B-----BBBBB-B-B-- ----B-BBBBBBBBBBBBBBB---BB-B--B--B-BBB--B-BBBBBB-BB------BB--B-B-B-BBBBBB -BBBBBBBBBB-BBB-B--------B--BBBBB----BBBBBBBBBBB-BB---BB--B-BBB--B--- ->JNETSOL5 ---------------BB--B--------B--BB--B------BB-BB------B--B-BB------B---B-- ----------B-----------------B--BB--B-------B------B--BB--BB-BBB--B---B--- ------B----------B---B-------B--BB-BB-B---B-BB--BB--B---------BB--B-B---- ----B-BBB-B-BB--BBB-B-------------------B-B-BB-B-B------------------B-B-B --B---B---B-B-----------------------------B--BBB--------------------- ->JNETSOL0 -------------------B-------------------------B--------------------B------ ----------------------------------------------------------B-B----B------- --------------------------------------B---B--B--B------------------------ ------B-----------------------------------------------------------------B --------------------------------------------------------------------- ->JNETHMM ------------HHHHHHHHHH-------HHHHHHHHHHHHHHH--------HHH---E----HHHHHHHHH- -----------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH -H--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------EEEEEEE--- ----EEE----EE----EEEE--------HHHHH--HH------EEEEEEEE-----------------HHHH -HHHHHHHHHHHH-----------------------------HHHHHH--------------------- ->JNETPSSM ------------HHHHHHHHHH-------HHHHHHHHHH-----------------EEE----HHHHHHHHH- -------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH- ----------HHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----EEEEEEE--H -HHHHHHHE---EE---EEEE---------H----HHHHH----HHHHHH-------EEE----------HHH -HHHHHHHHHHH-H-----------------------------HEEEE-----------------EE-- ->QUERY -SRMPSPPMPVPPAALFNRLLDDLGFSAGPALCTMLDTWNEDLFSALPTNADLYRECKFLSTLPSDVVEWGDA -YVPERTQIDIRAHGDVAFPTLPATRDGLGLYYEALSRFFHAELRAREESYRTVLANFCSALYRYLRASVRQL -HRQAHMRGRDRDLGEMLRATIADRYYRETARLARVLFLHLYLFLTREILWAAYAEQMMRPDLFDCLCCDLES -WRQLAGLFQPFMFVNGALTVRGVPIEARRLRELNHIREHLNLPLVRSAATEEPGAPLTTPPTLHGNQARASG -YFMVLIRAKLDSYSSFTTSPSEAVMREHAYSRAPTKNNYGSTIEGLLDLPDDDAPEEAGLAAPRLSFL ->UniRef90_Q00028 ------PPKATSPTALYQRLQAELGFPEGQAMLFAMEKWNEDMFSAIPVHVDLYTEIALLSTSVNEVVKAGLD -SLPIPTEVDLNAHGSEPFPEVPALEDELETYVISAQRFYLSELRAREEHYSRLLRGYCVALLHYLYGSAKRQ -LRGA---GSDSALMHKFKQVVRDRYYRETANLARLLYLHLYISVTREVSWRLHASQVVNQGIFVSLHYTWPQ -RRKFECLFHPVLFNHGVVILENDPLEFNDLQRINYRRRELGLPLIRAGLIEEENLPLESEPTFSGKLPRTIG -FLTHQIRTKMEAYSNAHPSTPLFPLAEHSYSRIDGRLSYGTTAEAMMDPPSPSA-------------- ->UniRef90_Q8B635 ------PIKASSPSSLIKNLLDELNFPEGPSLLSSMEKWNEDLFSCIPRFLEIYIENSILSTSVDEVIKNLDN -SLNYDDVIDFQVHGPETFPKTPLLEEELENYVTSVQKYFLSELKAREVTYSFLLTKYCKALLLYLRYNTKSS -IKG------NKDINQKFKQNVRERYYREVANIARLLYLHLYLSVTREVSWKLHADQVLLQSVFVSLSYSWSH -RRQFECIFHPILFNHGIVNLENNPLTFKELQKINYRRHILGLPLIRAGLVEEDNQPLMIPPEFSSKLPRTIG -FLTQQIRAKMEAYSDNHPVTPKFPRIEHSYAKPIDPINYGTTIEAMMDPPSPSA-------------- ->UniRef90_Q9E205 ------PPRVASPAVLYQQLINDLHFSEGPRIIALLETCNEDIFSCFPLNEDLYTDTIVFSTNPSDIIELETS -ETPE--PINLITKG-CDLPSLPSTYTELPMYVENVQNTFFTELRVREKAYLRLLILYCKSLLRHLQGISRRS -SVGARSQDCEHKYITQFKQSIRLRYYREVAKLARLLYLHLYITVTRQFSWRLFAQQSKYPDVFAAMKFMWLE -NRQFTCAFHPILCNHGIVLLEGKPLSSQRLREVNYRRRQLGLPLVRCALIEEKGVPLVQRPEFSAHMPRSLG -FLTHHIKAKLDVYSSKHSQEPGNVRVDHPYARNVNNINYGSSVEAMIVSPPSPS-------------- ->UniRef90_Q88530 ---LPSPE-AASPNLLYDRLILELDFAEGPSLLAKLERVNVDLFSCLPLNSHLYKHAKILSTCPREVLDAVYE -NTWQYTALNLNEHGKSSIPPVPASKDDLPAYVTAVQEFYLEELEAREQIYAKLFFGYCRALIMHIIKSV--L -NESRGVRVSDDYVQNKARWYISNNYYRDAVRIAKLLYLHLYLSTTEIVSQRLEAMQTSLQDLFVYLRCEWGQ -GRQFWCIFQPMIYNHGVPMIEGRALTSLELGSSNYIRSELGLPLIRCELLEELESPVVFPPTFTATAPRSSG -YLFHNIRAKMELYSNIHPSPQLSGLSDHTYVRTHVPVNYGTTVEVLLDASDPDS-------------- ->UniRef90_B4XS08 -------------------------FPEASTILSTFELMNMDLFSCLPRNEDLYRNAALLSGSVTEVIEA--S -EIPIDGEIDLNAHGSKQLPIPPSNEWEIPNYVEAVQQFFLSELRAREESYLKLFLGYCRAIVNYIKSAATRG -VRGCRIMDRKSEANKRMRRMIADRYYREAARLAKVLYLHLYLSVAREISSRLCATQMQVQNVFVYMRYEWQQ -YRQFTCLFHPIMFNHGVVLLNGEPLQAQKLREVNYIRFKLGLPVIRCGLVEEHDKPLVEEPRFYGNLPRSSG -FLTELIRSKMEAYSELRPTSPSSISNDHTYAKQLDKVNFGSTREAILDTIDTEGP------------- ->UniRef90_P09265 ----PSPPWVASPKILYQQLIRDLDFSEGPRLLSCLETWNEDLFSCFPINEDLYSDMMVLSPDPDDVI----S -TVSTKDHVNLTTRGSVRLPSPPKQPTGLPAYVQEVQDSFTVELRAREEAYTKLLVTYCKSIIRYLQGTAKRT -TIGLNIQNPDQKAYTQLRQSILLRYYREVASLARLLYLHLYLTVTREFSWRLYASQSAHPDVFAALKFTWTE -RRQFTCAFHPVLCNHGIVLLEGKPLTASALREINYRRRELGLPLVRCGLVEENKSPLVQQPSFSVHLPRSVG -FLTHHIKRKLDAYAVKHPQEPRHVRADHPYAKVVENRNYGSSIEAMILAP--PSPSE----------- ->UniRef90_Q2QBC8 -------------AALYNRLLEDLGFGDGPALCTILDSWNEDLFSGLPANPDLYRECRFLSTLPGDVVVWGDA -HAPDRGPIDIRAHGSAPFPSLPARREGLPAYCEALTRFFHSELRAREESYRRVLANFCSALYRYLRASTRQL -HRQAALKGRPRDLQEMLRAAVAERYYRETARLARVLFLHLYLFLVREILWAVYAEQVMRQDLFEGLRCDLEQ -ARQLSCLFQPLLFVHGALSVGGEPVSPARLRELNHVRERLNLPLIRSAATEEPGAALTAAPALQTQRARSSG -YFMTLIRVKLDAYSEWSAGSEGAVLREHAYSRRRERTNYGSSIEGLLEL------------------- ->UniRef90_Q90603 ----------------YTRLLHELDFVEGPSILARLEKINVDLFSCFPHNKHLYEHAKILSVSPSEVLEELSK -NTWTYTALNLNEHGEVALPMPPTTKADLPSYVDDIQNFYLGELEAREKSYATMFYGYCRALAEYIRQSAIKD -LRDA--RVEDKNIGACSKARQYIAERYYREAFANVLYVHLYLSTTRDVSQRLEASQMGRQNIFVYLKCEWLQ -ERHFHCLFQPVIFNHGVVIVEGRVLTAPELRAQNYIRSEFGLPLIRCKLVEEPDMPLISPPPFSGDAPRASV -YLLQCIRSKLEVYSSHPPNPQLHVHKEHVHQKLESPPNYGTTVEALLMDSSD---------------- ->UniRef90_O89246 ---------------------HELDFTEGPSLLSRLEKLNVDLFSCFPINGHLYEHATLLSVSPSEVLDAASE -EKWAYTAINLNEHCGMEVPRPPLTKDGLPVYVTEIQKFFSMELEAREKSYVTLLCGYCRALACYLRQGANEP -SRCDMCVGGS----ETPRRSIAGAYYREAARFARLLYMHLYLSVTRDVSRRLEASQRKRQNLFAHLRCDWHQ -LRHFQCLFQPVIFNHGVVIVEGRALTAAELRTQNYVRSELGLPVMRCELVEERGMPLTAPPAFLANAPRASA -YLFQCIKSKLEVYSLMHPPRPRSSARGESGRAGKAGPSHGTIVKAMLRDSTHPGPAIADIAAAR---- ->UniRef90_Q5PP87 -----------SPDALYQRLISDLAFDEGPALLGAMERWNEDLFSCLPGNEDLYARLVMLSASADEVAAQVRA -PTADAS-VDLGVPGAEPMPRVPAVEEELPAYVAAVERFFVSTLRAREERYARLLDAYCRAVLRYLHAQARRD --------------EGKLRQLVRGRYYRDVARLAPWLFLHLYVATARELSWRLHADQVVAQDVFMSLRYEWDQ -ARQLTCLFHPVLFNHGVVLLSGAPVPAAQLRAVNHRRRELGLPLVRAGLIEEDGADLVEEPPFSAALPRAAG -YLSHQVRIKMEAYS--------REYRDHTYCRPPSPVSYG---------------------------- ->UniRef90_Q65819 -----------------ERMQAELGFPDGPALLRAMERWNEDLFSCLPTNADLYADAALLSADADAVVGAMYL -AVPDAERLDLNAHANQPLPAPPASEEGLPEYVAGVQAHFLAELRAREERYAGLFLGYCRALLQHLRA----T -AARGRGAAGAGAQADRLRQLVAARYYREASRLARLAFAHMYVATAREVSWRLHSQQSQAQGVFVSLYYAWPQ -RRQFTCLFHPVLFNHGVVALEDGFLDAAELRRLNYRRRELGLPLVRAGLVEVEVGPLVEEPPFSGSLPRALG -FLNYQVRAKMGAPAE--AGGRLAPEREHSYARPRGAINYGTTPEAMLRPPSPS--------------- ->UniRef90_O56869 --RNPGPPALVSASFLAKNALTELQFADWDKIQHVLKTINIDIFSCVPVGENGLCNMDWFSLDTEKIWTLMDS -GTPNVSPNLLITPGPP--PECIKTPEEAPAYFEAISNYFESVLAAREAEYAKLLAEYAKSLAKYIRHKSQKV -GR--GLRALELDTEEAKKRLMKSEYYKGIEKLLIIFLVHLVLNACRDVARIIWVQQRDSSSVLQKVTYRWES --QQLHCIFQPLLVSPGPVFLDNDPLPLQTLQHVNYVRYLLGVPVLRFSMIEESPSAQYIP----YDKTAPSA -YDVLATIAR----TCLTSSGCSRASHDHTYARDNEKPNYSSSRIVLLADSALDTP------------- diff --git a/binaries/src/jpred/tests/res_d16vpa_.res.fasta b/binaries/src/jpred/tests/res_d16vpa_.res.fasta deleted file mode 100644 index 55507ce..0000000 --- a/binaries/src/jpred/tests/res_d16vpa_.res.fasta +++ /dev/null @@ -1,114 +0,0 @@ ->jnetpred ------------HHHHHHHHHH-------HHHHHHHHHHHHHHH-------------EE----HHHHHHHHH- -------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH -H--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------EEEEEEE--- -H-HHEE----EE----EEEE--------HHHHH--HHH-----EEEEE---------E----------HHHH -HHHHHHHHHHHH------------------------------HHHHH--------------------- ->JNETSOL25 ---------B-BB-BBB--BB--B-B--B--BB-BB--B-BBBBBBBBBB--BBBBB-BBBBBB--BB-BB-- --BB---BBBB-B-B---B--BB-----B--BB--B--BB---B-BBB--BB-BBB-BBBBBB-BB---B--- -B--B-B------B--BB-BBB---BB-BBB-BBBBBBBBBBBBBBBBBBBBBBB-B-----BBBBB-B-B-- ----B-BBBBBBBBBBBBBBB---BB-B--B--B-BBB--B-BBBBBB-BB------BB--B-B-B-BBBBBB -BBBBBBBBBB-BBB-B--------B--BBBBB----BBBBBBBBBBB-BB---BB--B-BBB--B--- ->JNETSOL5 ---------------BB--B--------B--BB--B------BB-BB------B--B-BB------B---B-- ----------B-----------------B--BB--B-------B------B--BB--BB-BBB--B---B--- ------B----------B---B-------B--BB-BB-B---B-BB--BB--B---------BB--B-B---- ----B-BBB-B-BB--BBB-B-------------------B-B-BB-B-B------------------B-B-B --B---B---B-B-----------------------------B--BBB--------------------- ->JNETSOL0 -------------------B-------------------------B--------------------B------ ----------------------------------------------------------B-B----B------- --------------------------------------B---B--B--B------------------------ ------B-----------------------------------------------------------------B --------------------------------------------------------------------- ->JNETHMM ------------HHHHHHHHHH-------HHHHHHHHHHHHHHH--------HHH---E----HHHHHHHHH- -----------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH -H--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------EEEEEEE--- ----EEE----EE----EEEE--------HHHHH--HH------EEEEEEEE-----------------HHHH -HHHHHHHHHHHH-----------------------------HHHHHH--------------------- ->JNETPSSM ------------HHHHHHHHHH-------HHHHHHHHHH-----------------EEE----HHHHHHHHH- -------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH- ----------HHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----EEEEEEE--H -HHHHHHHE---EE---EEEE---------H----HHHHH----HHHHHH-------EEE----------HHH -HHHHHHHHHHH-H-----------------------------HEEEE-----------------EE-- ->QUERY -SRMPSPPMPVPPAALFNRLLDDLGFSAGPALCTMLDTWNEDLFSALPTNADLYRECKFLSTLPSDVVEWGDA -YVPERTQIDIRAHGDVAFPTLPATRDGLGLYYEALSRFFHAELRAREESYRTVLANFCSALYRYLRASVRQL -HRQAHMRGRDRDLGEMLRATIADRYYRETARLARVLFLHLYLFLTREILWAAYAEQMMRPDLFDCLCCDLES -WRQLAGLFQPFMFVNGALTVRGVPIEARRLRELNHIREHLNLPLVRSAATEEPGAPLTTPPTLHGNQARASG -YFMVLIRAKLDSYSSFTTSPSEAVMREHAYSRAPTKNNYGSTIEGLLDLPDDDAPEEAGLAAPRLSFL ->UniRef90_Q00028 ------PPKATSPTALYQRLQAELGFPEGQAMLFAMEKWNEDMFSAIPVHVDLYTEIALLSTSVNEVVKAGLD -SLPIPTEVDLNAHGSEPFPEVPALEDELETYVISAQRFYLSELRAREEHYSRLLRGYCVALLHYLYGSAKRQ -LRGA---GSDSALMHKFKQVVRDRYYRETANLARLLYLHLYISVTREVSWRLHASQVVNQGIFVSLHYTWPQ -RRKFECLFHPVLFNHGVVILENDPLEFNDLQRINYRRRELGLPLIRAGLIEEENLPLESEPTFSGKLPRTIG -FLTHQIRTKMEAYSNAHPSTPLFPLAEHSYSRIDGRLSYGTTAEAMMDPPSPSA-------------- ->UniRef90_Q8B635 ------PIKASSPSSLIKNLLDELNFPEGPSLLSSMEKWNEDLFSCIPRFLEIYIENSILSTSVDEVIKNLDN -SLNYDDVIDFQVHGPETFPKTPLLEEELENYVTSVQKYFLSELKAREVTYSFLLTKYCKALLLYLRYNTKSS -IKG------NKDINQKFKQNVRERYYREVANIARLLYLHLYLSVTREVSWKLHADQVLLQSVFVSLSYSWSH -RRQFECIFHPILFNHGIVNLENNPLTFKELQKINYRRHILGLPLIRAGLVEEDNQPLMIPPEFSSKLPRTIG -FLTQQIRAKMEAYSDNHPVTPKFPRIEHSYAKPIDPINYGTTIEAMMDPPSPSA-------------- ->UniRef90_Q9E205 ------PPRVASPAVLYQQLINDLHFSEGPRIIALLETCNEDIFSCFPLNEDLYTDTIVFSTNPSDIIELETS -ETPE--PINLITKG-CDLPSLPSTYTELPMYVENVQNTFFTELRVREKAYLRLLILYCKSLLRHLQGISRRS -SVGARSQDCEHKYITQFKQSIRLRYYREVAKLARLLYLHLYITVTRQFSWRLFAQQSKYPDVFAAMKFMWLE -NRQFTCAFHPILCNHGIVLLEGKPLSSQRLREVNYRRRQLGLPLVRCALIEEKGVPLVQRPEFSAHMPRSLG -FLTHHIKAKLDVYSSKHSQEPGNVRVDHPYARNVNNINYGSSVEAMIVSPPSPS-------------- ->UniRef90_Q88530 ---LPSPE-AASPNLLYDRLILELDFAEGPSLLAKLERVNVDLFSCLPLNSHLYKHAKILSTCPREVLDAVYE -NTWQYTALNLNEHGKSSIPPVPASKDDLPAYVTAVQEFYLEELEAREQIYAKLFFGYCRALIMHIIKSV--L -NESRGVRVSDDYVQNKARWYISNNYYRDAVRIAKLLYLHLYLSTTEIVSQRLEAMQTSLQDLFVYLRCEWGQ -GRQFWCIFQPMIYNHGVPMIEGRALTSLELGSSNYIRSELGLPLIRCELLEELESPVVFPPTFTATAPRSSG -YLFHNIRAKMELYSNIHPSPQLSGLSDHTYVRTHVPVNYGTTVEVLLDASDPDS-------------- ->UniRef90_B4XS08 -------------------------FPEASTILSTFELMNMDLFSCLPRNEDLYRNAALLSGSVTEVIEA--S -EIPIDGEIDLNAHGSKQLPIPPSNEWEIPNYVEAVQQFFLSELRAREESYLKLFLGYCRAIVNYIKSAATRG -VRGCRIMDRKSEANKRMRRMIADRYYREAARLAKVLYLHLYLSVAREISSRLCATQMQVQNVFVYMRYEWQQ -YRQFTCLFHPIMFNHGVVLLNGEPLQAQKLREVNYIRFKLGLPVIRCGLVEEHDKPLVEEPRFYGNLPRSSG -FLTELIRSKMEAYSELRPTSPSSISNDHTYAKQLDKVNFGSTREAILDTIDTEGP------------- ->UniRef90_P09265 ----PSPPWVASPKILYQQLIRDLDFSEGPRLLSCLETWNEDLFSCFPINEDLYSDMMVLSPDPDDVI----S -TVSTKDHVNLTTRGSVRLPSPPKQPTGLPAYVQEVQDSFTVELRAREEAYTKLLVTYCKSIIRYLQGTAKRT -TIGLNIQNPDQKAYTQLRQSILLRYYREVASLARLLYLHLYLTVTREFSWRLYASQSAHPDVFAALKFTWTE -RRQFTCAFHPVLCNHGIVLLEGKPLTASALREINYRRRELGLPLVRCGLVEENKSPLVQQPSFSVHLPRSVG -FLTHHIKRKLDAYAVKHPQEPRHVRADHPYAKVVENRNYGSSIEAMILAP--PSPSE----------- ->UniRef90_Q2QBC8 -------------AALYNRLLEDLGFGDGPALCTILDSWNEDLFSGLPANPDLYRECRFLSTLPGDVVVWGDA -HAPDRGPIDIRAHGSAPFPSLPARREGLPAYCEALTRFFHSELRAREESYRRVLANFCSALYRYLRASTRQL -HRQAALKGRPRDLQEMLRAAVAERYYRETARLARVLFLHLYLFLVREILWAVYAEQVMRQDLFEGLRCDLEQ -ARQLSCLFQPLLFVHGALSVGGEPVSPARLRELNHVRERLNLPLIRSAATEEPGAALTAAPALQTQRARSSG -YFMTLIRVKLDAYSEWSAGSEGAVLREHAYSRRRERTNYGSSIEGLLEL------------------- ->UniRef90_Q90603 ----------------YTRLLHELDFVEGPSILARLEKINVDLFSCFPHNKHLYEHAKILSVSPSEVLEELSK -NTWTYTALNLNEHGEVALPMPPTTKADLPSYVDDIQNFYLGELEAREKSYATMFYGYCRALAEYIRQSAIKD -LRDA--RVEDKNIGACSKARQYIAERYYREAFANVLYVHLYLSTTRDVSQRLEASQMGRQNIFVYLKCEWLQ -ERHFHCLFQPVIFNHGVVIVEGRVLTAPELRAQNYIRSEFGLPLIRCKLVEEPDMPLISPPPFSGDAPRASV -YLLQCIRSKLEVYSSHPPNPQLHVHKEHVHQKLESPPNYGTTVEALLMDSSD---------------- ->UniRef90_O89246 ---------------------HELDFTEGPSLLSRLEKLNVDLFSCFPINGHLYEHATLLSVSPSEVLDAASE -EKWAYTAINLNEHCGMEVPRPPLTKDGLPVYVTEIQKFFSMELEAREKSYVTLLCGYCRALACYLRQGANEP -SRCDMCVGGS----ETPRRSIAGAYYREAARFARLLYMHLYLSVTRDVSRRLEASQRKRQNLFAHLRCDWHQ -LRHFQCLFQPVIFNHGVVIVEGRALTAAELRTQNYVRSELGLPVMRCELVEERGMPLTAPPAFLANAPRASA -YLFQCIKSKLEVYSLMHPPRPRSSARGESGRAGKAGPSHGTIVKAMLRDSTHPGPAIADIAAAR---- ->UniRef90_Q5PP87 -----------SPDALYQRLISDLAFDEGPALLGAMERWNEDLFSCLPGNEDLYARLVMLSASADEVAAQVRA -PTADAS-VDLGVPGAEPMPRVPAVEEELPAYVAAVERFFVSTLRAREERYARLLDAYCRAVLRYLHAQARRD --------------EGKLRQLVRGRYYRDVARLAPWLFLHLYVATARELSWRLHADQVVAQDVFMSLRYEWDQ -ARQLTCLFHPVLFNHGVVLLSGAPVPAAQLRAVNHRRRELGLPLVRAGLIEEDGADLVEEPPFSAALPRAAG -YLSHQVRIKMEAYS--------REYRDHTYCRPPSPVSYG---------------------------- ->UniRef90_Q65819 -----------------ERMQAELGFPDGPALLRAMERWNEDLFSCLPTNADLYADAALLSADADAVVGAMYL -AVPDAERLDLNAHANQPLPAPPASEEGLPEYVAGVQAHFLAELRAREERYAGLFLGYCRALLQHLRA----T -AARGRGAAGAGAQADRLRQLVAARYYREASRLARLAFAHMYVATAREVSWRLHSQQSQAQGVFVSLYYAWPQ -RRQFTCLFHPVLFNHGVVALEDGFLDAAELRRLNYRRRELGLPLVRAGLVEVEVGPLVEEPPFSGSLPRALG -FLNYQVRAKMGAPAE--AGGRLAPEREHSYARPRGAINYGTTPEAMLRPPSPS--------------- ->UniRef90_O56869 --RNPGPPALVSASFLAKNALTELQFADWDKIQHVLKTINIDIFSCVPVGENGLCNMDWFSLDTEKIWTLMDS -GTPNVSPNLLITPGPP--PECIKTPEEAPAYFEAISNYFESVLAAREAEYAKLLAEYAKSLAKYIRHKSQKV -GR--GLRALELDTEEAKKRLMKSEYYKGIEKLLIIFLVHLVLNACRDVARIIWVQQRDSSSVLQKVTYRWES --QQLHCIFQPLLVSPGPVFLDNDPLPLQTLQHVNYVRYLLGVPVLRFSMIEESPSAQYIP----YDKTAPSA -YDVLATIAR----TCLTSSGCSRASHDHTYARDNEKPNYSSSRIVLLADSALDTP------------- diff --git a/binaries/src/jpred/tests/todo.bash b/binaries/src/jpred/tests/todo.bash index 030ea8a..47417f2 100755 --- a/binaries/src/jpred/tests/todo.bash +++ b/binaries/src/jpred/tests/todo.bash @@ -21,9 +21,11 @@ ln -s /data/UNIREFdb databases #################################################################################################### -../jpred.pl -seq d16vpa_.fas -o res_d16vpa_ -dbname ported_db -dbpath /data/UNIREFdb/ -ncpu 4 -debug -../jpred.pl -seq SCOP175B_nr.seq -o res_SCOP175B_nr -dbname ported_db -dbpath /data/UNIREFdb/ -ncpu 4 -debug -../jpred.pl -seq T-state1.fas -o res_T-state1.res -dbname ported_db -dbpath /data/UNIREFdb/ -ncpu 4 -debug -../jpred.pl -seq T-state2.fas -o res_T-state2.res -dbname ported_db -dbpath /data/UNIREFdb/ -ncpu 4 -debug +../jpred.pl -seq -in d16vpa_.fas -outfile d16vpa_.res.fasta -dbname ported_db -dbpath /data/UNIREFdb/ -ncpu 4 -debug +../jpred.pl -seq -in d1b3aa_.fas -outfile d1b3aa_.res.fasta -dbname ported_db -dbpath /data/UNIREFdb/ -ncpu 4 -debug +../jpred.pl -seq -in T-state1.fas -outfile res_T-state1.res.fasta -dbname ported_db -dbpath /data/UNIREFdb/ -ncpu 4 -debug +../jpred.pl -seq -in T-state2.fas -outfile res_T-state2.res.fasta -dbname ported_db -dbpath /data/UNIREFdb/ -ncpu 4 -debug -./webscripts/fasta2concise < d16vpa_.res.align > d16vpa_.res.align.csv +../jpred.pl -in alignment.msf -outfile alignment_from_msf.res.fasta -dbname ported_db -dbpath /data/UNIREFdb/ -ncpu 4 -debug +../jpred.pl -in alignment.blc -outfile alignment_from_blc.res.fasta -dbname ported_db 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