PRSS3(1)PRSS3(1)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 pro‐
tein: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 sim‐
ilarity scores was described by Altshul and Karlin, PNAS (1990)
87:2264-2268. The and expectations calculated by prdf. prss34 calcu‐
lates 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 penal‐
ties, 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 like‐
lihood 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 pro‐
tein 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).
SEE ALSOssearch3(1), fasta3(1).
AUTHOR
Bill Pearson
wrp@virginia.EDU
local PRSS3(1)
