RSS(1)RSS(1)NAMEprss - test a protein sequence similarity for significance
SYNOPSISprss [-Q-f # -g # -h-O file -s SMATRIX -w # ] sequence-file-1
sequence-file-2 [ #-of-shuffles ]
prss [-fghsw] - interactive mode
DESCRIPTIONprss is used to evaluate the significance of a protein sequence simi‐
larity score by comparing two sequences and calculating optimal simi‐
larity scores, and then repeatedly shuffling the second sequence, and
calculating optimal similarity scores using the Smith-Waterman algo‐
rithm. 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 pro‐
gram is derived from rdf2, which was 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 sim‐
ilarity 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. prss uses calcu‐
lates optimal scores using the same rigorous Smith-Waterman algorithm
(Smith and Waterman, J. Mol. Biol. (1983) 147:195-197) used by the
ssearch program.
prss also allows 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) prss-w 10 musplfm.aa lcbo.aa
Compare the amino acid sequence in the file musplfm.aa with that in
lcbo.aa, then shuffle lcbo.aa 100 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) prss musplfm.aa lcbo.aa
Compare the amino acid sequence in the file musplfm.aa with the
sequences in the file lcbo.aa.
(3) prss
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. 100 shuffles are calculated by default; 250 - 500 shuffles
should provide more accurate probability estimates.
OPTIONSprss 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.
-f # Penalty for the first residue in a gap (-12 by default).
-g # Penalty for additional residues in a gap (-2 by default).
-h Do not display histogram of similarity scores.
-Q -q "quiet" - do not prompt for filename.
-O filename
send copy of results to "filename."
-s str (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 250(or with -s
pam250.mat).
SEE ALSOssearch(1), prdf(1), fasta(1), lfasta(1), protcodes(5)AUTHOR
Bill Pearson
wrp@virginia.EDU
The curve fitting routines in rweibull.c were provided by Phil Green,
Washington U., St. Louis.
local RSS(1)
