mlocalS
NAME
mlocalS - compare two sequences, using a penalty matrix, to
find best-scoring local alignments.
SYNOPSIS
mlocalS db file2 matrix csub alpha beta [ flags ]
DESCRIPTION
mlocalS finds the best local alignments between sequences in
db and the sequence in file2 using penalty matrix matrix,
along with scoring parameters csub, alpha and beta, and
reports those non-intersecting local alignments having a
cutoff score of at least # if the -c# option is specified,
or # of non-intersecting local alignments with highest
scores if the -n# option is specified.
The format of sequence files db and file2 is our standard
format, the Pearson/FASTA format. The first line is the
sequence name, and should be used as a description. Subse-
quent lines contain the sequence to be used. The sequences
themselves may contain blanks, returns, and other whitespace
for readability. The sequence terminates at end-of-file,
`>' is read to begin a new sequence in the FASTA format.
Only multiple sequences in the first file will be processed.
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 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.
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), srlocalS(1), msrlocalS(1)
, trlo-
calS(1), mtrlocalS
(1), pvlocalS(1), <
STRONG>mpvlocalS(1), penalty-
matrix(5), sequ
ence-file(5).