+++ /dev/null
-.TH PRSS3 1 local
-.SH NAME
-prss \- test a protein sequence similarity for significance
-.SH SYNOPSIS
-.B prss34
-\&[-Q -A -f # -g # -H -O file -s SMATRIX -w # -Z #
-.I -k # -v #
-]
-sequence-file-1 sequence-file-2
-[
-.I #-of-shuffles
-]
-
-.B prfx34
-\&[-Q -A -f # -g # -H -O file -s SMATRIX -w # -z 1,3 -Z #
-.I -k # -v #
-]
-sequence-file-1 sequence-file-2
-[
-.I ktup
-]
-[
-.I #-of-shuffles
-]
-
-.B prss34(_t)/prfx34(_t)
-[-AfghksvwzZ]
-\- interactive mode
-
-.SH DESCRIPTION
-.B prss34
-and
-.B prfx34
-are used to evaluate the significance of a protein:protein, DNA:DNA
-(
-.B prss34
-), or translated-DNA:protein (
-.B prfx34
-) sequence similarity score
-by comparing two sequences and calculating optimal similarity scores,
-and then repeatedly shuffling the second sequence, and calculating
-optimal similarity scores using the Smith-Waterman algorithm. An
-extreme value distribution is then fit to the shuffled-sequence
-scores. The characteristic parameters of the extreme value
-distribution are then used to estimate the probability that each of
-the unshuffled sequence scores would be obtained by chance in one
-sequence, or in a number of sequences equal to the number of shuffles.
-This program is derived from
-.B rdf2\c
-\&, described by Pearson and Lipman, PNAS (1988) 85:2444-2448, and
-Pearson (Meth. Enz. 183:63-98). Use of the extreme value
-distribution for estimating the probabilities of similarity scores was
-described by Altshul and Karlin, PNAS (1990) 87:2264-2268. The
-'z-values' calculated by rdf2 are not as informative as the P-values
-and expectations calculated by prdf.
-.B prss34
-calculates optimal scores using the same rigorous Smith-Waterman
-algorithm (Smith and Waterman, J. Mol. Biol. (1983) 147:195-197) used by the
-.B ssearch34
-program.
-.B prfx34
-calculates scores using the FASTX algorithm (Pearson et al. (1997) Genomics 46:24-36.
-.PP
-.B prss34
-and
-.B prfx34
-also allow a more sophisticated shuffling method: residues can be shuffled
-within a local window, so that the order of residues 1-10, 11-20, etc,
-is destroyed but a residue in the first 10 is never swapped with a residue
-outside the first ten, and so on for each local window.
-.SH EXAMPLES
-.TP
-(1)
-.B prss34
-\& -v 10 musplfm.aa lcbo.aa
-.PP
-Compare the amino acid sequence in the file musplfm.aa with that
-in lcbo.aa, then shuffle lcbo.aa 200 times using a local shuffle with
-a window of 10. Report the significance of the
-unshuffled musplfm/lcbo comparison scores with respect to the shuffled
-scores.
-.TP
-(2)
-.B prss34
-musplfm.aa lcbo.aa 1000
-.PP
-Compare the amino acid sequence in the file musplfm.aa with the sequences
-in the file lcbo.aa, shuffling \fClcbo.aa\fP 1000 times. Shuffles can also be specified with the -k # option.
-.TP
-(3)
-.B prfx34
-mgstm1.esq xurt8c.aa 2 1000
-.PP
-Translate the DNA sequence in the \fCmgstm1.esq\fP file in all six
-frames and compare it to the amino acid sequence in the file
-\fCxurt8c.aa\fP, using ktup=2 and shuffling \fCxurt8c.aa\fP 1000
-times. Each comparison considers the best forward or reverse
-alignment with frameshifts, using the fastx algorithm (Pearson et al
-(1997) Genomics 46:24-36).
-.TP
-(4)
-.B prss34/prfx34
-.PP
-Run prss in interactive mode. The program will prompt for the file
-name of the two query sequence files and the number of shuffles to be
-used.
-.SH OPTIONS
-.PP
-.B prss34/prfx34
-can be directed to change the scoring matrix, gap penalties, and
-shuffle parameters by entering options on the command line (preceeded
-by a `\-'). All of the options should preceed the file names number of
-shuffles.
-.TP
-\-A
-Show unshuffled alignment.
-.TP
-\-f #
-Penalty for opening a gap (-10 by default for proteins).
-.TP
-\-g #
-Penalty for additional residues in a gap (-2 by default) for proteins.
-.TP
-\-H
-Do not display histogram of similarity scores.
-.TP
-\-k #
-Number of shuffles (200 is the default)
-.TP
-\-Q -q
-"quiet" - do not prompt for filename.
-.TP
-\-O filename
-send copy of results to "filename."
-.TP
-\-s str
-specify the scoring matrix. BLOSUM50 is used by default for proteins;
-+5/-4 is used by defaul for DNA.
-.B prss34
-recognizes the same scoring matrices as fasta34, ssearch34, fastx34, etc;
-e.g. BL50, P250, BL62, BL80, MD10, MD20, and other matrices in BLAST1.4
-matrix format.
-.TP
-\-v #
-Use a local window shuffle with a window size of #.
-.TP
-\-z #
-Calculate statistical significance using the mean/variance
-(moments) approach used by fasta34/ssearch or from maximum likelihood
-estimates of lambda and K.
-.TP
-\-Z #
-Present statistical significance as if a '#' entry database had
-been searched (e.g. "-Z 50000" presents statistical significance as if
-50,000 sequences had been compared).
-.SH ENVIRONMENT VARIABLES
-.PP
-.B (SMATRIX)
-the filename of an alternative scoring matrix file. For protein
-sequences, BLOSUM50 is used by default; PAM250 can be used with the
-command line option
-.B -s P250\c
-(or with -s pam250.mat). BLOSUM62 (-s BL62) and PAM120 (-S P120).
-.SH "SEE ALSO"
-ssearch3(1), fasta3(1).
-.SH AUTHOR
-Bill Pearson
-.br
-wrp@virginia.EDU
-
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