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-.TH PVCOMPFA/PVCOMPSW/v3.4 1 "January, 2003"
-.SH NAME
-.B pv34compfa
-\- scan a protein or DNA sequence library for similar
-sequences using the FASTA algorithm in parallel on a network of
-machines running pvm3.
-
-.B pv34compsw
-\- scan a protein or DNA sequence library for similar
-sequences using the Smith-Waterman algorithm in parallel on a network
-of machines running pvm3.
-
-.B ps34compfa
-\- evaluate sequence comparison parameters using the FASTA
-algorithm and super-family-annotated libraries.
-
-.B ps34compsw
-\- evaluate sequence comparison parameters using the
-Smith-Waterman algorithm and super-family-annotated libraries.
-
-.SH SYNOPSIS
-.B pv34compfa
-[-Q|q -B -b # -d # -E # -f # -g # -H -i J # -n -o -p #
-\& -R
-.I STATFILE
-\& -r "+n/-m" \& -S -s
-.I SMATRIX
-\& -w # -1 ] query-library reference-library [
-.I ktup
-]
-.B pv34compfa
-[\-QBbcefgHiJnopRrSsw1] \- interactive mode
-
-.B pv34compsw
-[-Q|q -B -b # -e -f delval -g gapval -i
-\& -n -p # -R -R
-.I STATFILE
-\& -r "+n/-m" \& -S -s
-\& -s
-.I SMATRIX
- ] query-library reference-library [
-.I ktup
-]
-
-.B pv34compsw
-[\-QBbefgnpRrsS] \- interactive mode
-
-.SH DESCRIPTION
-.B pv34compfa
-and
-.B pv34compsw
-compare all of the sequences in one DNA or protein sequence library
-(the query library) with to all of the entries in a reference sequence
-library using the FASTA (pv34compfa) or Smith-Waterman (pv34compsw)
-algorithms. For example,
-.B pv34compfa
-can compare a library of protein sequences to all of the sequences in
-the NBRF PIR protein sequence database.
-.B pv34compfa
-and
-.B pv34compsw
-are designed to run in parallel on networks of unix workstations using
-the PVM parallel programming system. (For more information on PVM,
-send email to "netlib@ornl.gov" with the message "send index for pvm3").
-.PP
-.B pv34compfa
-uses the rapid sequence comparison algorithm
-described in Pearson and Lipman, Proc. Natl. Acad. USA, (1988) 85:2444.
-The program can be invoked either with command line arguments or in
-interactive mode. The optional third argument,
-.I ktup
-sets the sensitivity and speed of the search. If
-.I ktup=2,
-similar regions in the two sequences being compared are found by
-looking at pairs of aligned residues; if
-.I ktup=1,
-single aligned amino acids are examined.
-.I ktup
-can be set to 2 or 1 for protein sequences, or from 1 to 6 for DNA sequences.
-The default if
-.I
-ktup
-is not specified is 2 for proteins and 6 for DNA.
-.PP
-.B pv34compfa
-compares a library of query sequences (there need be only one) to a
-reference sequence library. Normally
-.B pv34compfa
-sorts the output by the
-.I initn
-score. By using the
-.I \-1
-option, sequences are ranked by their
-.B init1
-score. Alternative, the
-.I \-o
-option causes optimized scores to be calculated for every sequence
-greater than a threshold and the output to be sorted by the optimized
-scores.
-.PP
-.B pv34compsw
-uses the rigorous Smith-Waterman algorithm to compare protein or
-DNA sequences. The gap penalties and scoring matrices can be
-modified with the
-.I -f\c
-\&,
-.I -k\c
-\&, and
-.I -s
-options.
-.PP
-.B pv34compfa
-(and
-.B pv34compsw\c
-\&) will automatically decide whether the query sequence is DNA or
-protein by reading the query sequence as protein and determining
-whether the `amino-acid composition' is more than 85% A+C+G+T.
-.PP
-.B ps34compfa
-and
-.B ps34compsw
-are versions of
-.B pv34compfa
-and
-.B pv34compsw
-that evaluate the quality of a search by reporting how many
-high-scoring related sequences and low-scoring unrelated sequences
-were found. These programs require that both the query library and
-the reference library be annotated with superfamily numbers for every
-sequence in the library.
-.SH OPTIONS
-.LP
-.B Pv34compfa
-and
-.B pv34compsw
-now support all the options of the fasta3(_t) programs.
-.TP
-\-B
-Report z-score, rather than bit-score, in list of best hits.
-.TP
-\-b #
-The number of similarity scores to be shown (10 by default).
-.TP
-\-E #
-Expectation value limit for displaying best scores.
-.TP
-\-d #
-The number of alignments to be shown.
-.TP
-\-f #
-(delval) penalty for the first residue in a gap. -12 by default for proteins.
-.TP
-\-g #
-(gapval) penalty for additional residues in a gap after the first. -2
-by default for proteins.
-.TP
-\-H #
-turn on histogram display (off by default).
-.TP
-\-i
-invert (reverse complement) DNA sequence.
-.TP
-\-J M:N
-start at the M-th sequence in the query library and continue to the
-"N-th". By default, J=1 and the search begins with the first sequence
-and ends with the last, but sometimes it makes sense to start in the
-middle of the query library if a run partially completed, and to
-finish "early" if the analysis will be run on several parallel
-clusters.
-.TP
-\-n
-Force the program to use DNA sequence parameters.
-.TP
-\-p #
-Number of "slave" processors to use. Typically, one less than
-the number of processors available with
-.B pv34compfa
-so that one processor can be used to collate results. With
-.B pv34compsw\c
-\&, it is more efficient to use every processor as a slave and
-not use this option.
-.TP
-\-Q \-q
-Quiet option. The programs will not prompt for input.
-.TP
-\-R file
-(STATFILE) Causes
-.B pv34compfa
-and
-.B pv34compsw
-to write out the sequence identifier, superfamily number (if available),
-and similarity scores to
-.I STATFILE
-for every sequence in the library. These results are not sorted.
-.TP
-\-r
-specify DNA match/mismatch ratio as "+3/-2". Default is "+5/-4".
-The "+" and "-" are required.
-.TP
-\-S
-Treat lower case residues as low complexity regions.
-.TP
-\-s file
-the filename of an alternative scoring matrix file.
-.LP
-.B
-pv34compfa
-only
-.TP
-\-1
-sort similarity scores by
-.I init1
-scores instead of
-.I initn
-scores.
-.TP
-\-c #
-(OPTCUT) the threshold for optimization with the
-.B -o
-option.
-.TP
-\-o
-(no-optimize); causes
-.B pv34compfa
-not to perform the default optimization on all of the sequences in the library
-with
-.B initn
-scores greater than
-.B OPTCUT\c
-\&.
-.TP
-\-y #
-Width for limited optimization (32 by default).
-.SH FILES
-.LP
-Query library files must be in Pearson/FASTA format, e.g.
-.in +0.5i
-.nf
->seq-id | sfnum descriptive line
-tmlyrghi... (sequence)
-
-.fi
-.in -0.5i
-.PP
-.B pv34compfa
-and
-.B pv34compsw
-recognize the following library formats: 0 - Pearson/FASTA; 1 - Genbank tape;
-2 - NBRF/PIR Codata; 3 - EMBL/SWISS-PROT; 5 - NBRF/PIR VMS.
-.PP
-.I Scoring matrices \-
-These programs use a different format for the scoring (PAM) matrix
-file from FASTA; they use the PAM matrix file that is used by BLASTP
-and produced by Altshul's "pam.c" program in the BLAST package.
-.SH BUGS
-The program has been tested extensively only with type 0 and type 5
-files. This documentation file may not be up to date.
-.SH AUTHOR
-Bill Pearson
-.br
-wrp@virginia.EDU
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