msrlocalS
NAME
msrlocalS - finds self-repeats in a sequence, using similar-
ity scoring with a penalty matrix.
SYNOPSIS
msrlocalS file matrix csub alpha beta [ flags ]
DESCRIPTION
msrlocalS looks for self-repeats of subsequences in the
sequence in file (given a particular set of scoring parame-
ters), using a penalty matrix, and reports those repeat
alignments having a cutoff score of at least # if the -c#
option is specified, or with # of repeat local alignments
with highest scores if the -n# option is specified.
The scoring parameters are all integer values, and all posi-
tive.
csub is the lower limit for conservative substitutions,
which are non-matching substitutions printed with
a `:' in alignment output.
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), srlocalS(1),
STRONG> trlo-
calS(1), mtrlocalS
(1), pvlocalS(1), <
STRONG>mpvlocalS(1), penalty-
matrix(5), sequ
ence-file(5).