trlocalS
NAME
trlocalS - look for tandem repeats of a specified pattern in
a sequence
SYNOPSIS
trlocalS db pattern match mismatch alpha [ flags ]
DESCRIPTION
trlocalS looks for tandem repeats of a given pattern in the
sequence in file (given a particular set of scoring parame-
ters), and reports the best score.
The scoring parameters are all integer values, and all posi-
tive. The parameters mismatch and alpha are subtracted 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 each letter of an
insertion or deletion sequence (indel).
flags See manual page seqaln-intro (1) for a full
description of optional flags.
The format of the sequence file db is our standard format,
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, beginning a new sequence in FASTA format. Multiple
sequences in this file will be processed.
REFERENCES
E. Myers and W. Miller. "Approximate matching of regular
expressions. Bull. Math. Biol. (1989). 51:5-37.
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> srlo-
calS(1), mtrlocalS
(1), pvlocalS(1), mpvlocalS(1), sequence-
file(5).