mtrlocalS
NAME
mtrlocalS - look for tandem repeats of a specified pattern
in a sequence using a penalty matrix
SYNOPSIS
mtrlocalS db pattern matrix csub alpha [ flags ]
DESCRIPTION
mtrlocalS looks for tandem repeats of a given pattern in the
sequence in file (given a particular set of scoring parame-
ters), using a penalty matrix, and reports the best score.
matrix is a lower-diagonal penalty matrix with 26 rows
and columns, corresponding to the 26 letters of
the alphabet. This allows matrices to be built
for protein, DNA, and RNA sequences depending upon
the letters used. The most common use of this
matrix is to compare amino acid sequences in pro-
teins, but the flexibility of the matrix input
allows other types of sequences to be compared.
The matrix file name ends in ".mat"; this suffix
is not given. If the matrix is not found in the
current directory, the directory given by the
environment variable MATDIR will be examined.
csub is the lower limit for conservative substitutions,
which are non-matching substitutions printed with
a `:' in alignment output.
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), trlocalS(1
), pvlocalS(1), mpvlocalS(1), penalty-
matrix(5), sequ
ence-file(5).