srlocalS
NAME
srlocalS - look for self-repeats in a sequence, using simi-
larity scoring.
SYNOPSIS
srlocalS file match mismatch alpha beta [ flags ]
DESCRIPTION
srlocalS looks for self-repeats of subsequences in the
sequence in file (given a particular set of scoring parame-
ters), and reports those repeat alignments having a cutoff
score of at least # if the -c# option is specified, or with
# repeat local alignments with highest scores if the - n#
option is specified.
The scoring parameters are all integer values, and all posi-
tive. The parameters mismatch, alpha and beta are sub-
tracted from the score; match is added to the score.
match the score for aligning identical letters.
mismatch the amount to subtract for a mismatch.
alpha the amount to subtract for the first letter of an
insertion or deletion sequence (indel).
beta is the amount to subtract for subsequent letters
in an indel. For example, if there is a five-
letter indel, k = 5, then alpha + beta * ( k - 1 )
= alpha + beta * (4) will be subtracted from the
score.
flags See manual page seqaln-intro (1) for a full
description of optional flags.
The format of the sequence file file is our standard format,
or the Pearson/FASTA format. The first line is the sequence
name, and should be used as a description. Subsequent lines
contain the sequence to be used. The sequences themselves
may contain blanks, returns, and other whitespace for reada-
bility. The sequence terminates at end-of-file, or if `//'
is read in our format or `>' is read in the Pearson format.
REFERENCES
T.F. Smith and M.S. Waterman. "Identification of Common
Molecular Subsequences". Journal of Molecular Biology,
147, (1981) 195.
M.S. Waterman and M. Eggert. "A New Algorithm for Best
Subsequence Alignments with Application to tRNA-rRNA
Comparisons". Journal of Molecular Biology 197 (1987)
723-728.
M.S. Waterman. Introduction to Computational Biology: Maps,
sequences and genomes. Chapman & Hall. London: 1995. ISBN
0-412-99391-0.
SEE ALSO
seqaln-intro(1), localS(1), mlocalS(1), msrlocalS(1),<
/STRONG> trlo-
calS(1), mtrlocalS
(1), pvlocalS(1), mpvlocalS(1), sequence-
file(5).