NAME

prss - test a protein sequence similarity for significance

SYNOPSIS

prss34 [-Q -A -f # -g # -H -O file -s SMATRIX -w # -Z # -k # -v # ] sequence-file-1 sequence-file-2 [ #-of-shuffles ]

prfx34 [-Q -A -f # -g # -H -O file -s SMATRIX -w # -z 1,3 -Z # -k # -v # ] sequence-file-1 sequence-file-2 [ ktup ] [ #-of-shuffles ]

prss34(_t)/prfx34(_t) [-AfghksvwzZ] - interactive mode

DESCRIPTION

prss34 and prfx34 are used to evaluate the significance of a protein:protein, DNA:DNA ( prss34 ), or translated-DNA:protein ( 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 rdf2, 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 and expectations calculated by prdf. prss34 calculates optimal scores using the same rigorous Smith-Waterman algorithm (Smith and Waterman, J. Mol. Biol. (1983) 147:195-197) used by the ssearch34 program. prfx34 calculates scores using the FASTX algorithm (Pearson et al. (1997) Genomics 46:24-36.

prss34 and 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.

EXAMPLES

(1): prss34 -v 10 musplfm.aa lcbo.aa

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.

(2): prss34 musplfm.aa lcbo.aa 1000

Compare the amino acid sequence in the file musplfm.aa with the sequences in the file lcbo.aa, shuffling lcbo.aa 1000 times. Shuffles can also be specified with the -k # option.

(3): prfx34 mgstm1.esq xurt8c.aa 2 1000

Translate the DNA sequence in the mgstm1.esq file in all six frames and compare it to the amino acid sequence in the file xurt8c.aa, using ktup=2 and shuffling xurt8c.aa 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).

(4): prss34/prfx34

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.

OPTIONS

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.

-A: Show unshuffled alignment.
-f #: Penalty for opening a gap (-10 by default for proteins).
-g #: Penalty for additional residues in a gap (-2 by default) for proteins.
-H: Do not display histogram of similarity scores.
-k #: Number of shuffles (200 is the default)
-Q -q: "quiet" - do not prompt for filename.
-O filename: send copy of results to "filename."
-s str: specify the scoring matrix. BLOSUM50 is used by default for proteins; +5/-4 is used by defaul for DNA. 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.
-v #: Use a local window shuffle with a window size of #.
-z #: Calculate statistical significance using the mean/variance (moments) approach used by fasta34/ssearch or from maximum likelihood estimates of lambda and K.
-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).

ENVIRONMENT VARIABLES

(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 -s P250(or with -s pam250.mat). BLOSUM62 (-s BL62) and PAM120 (-S P120).

AUTHOR

Bill Pearson
wrp@virginia.EDU