localS
NAME
localS - compare two sequences to find best-scoring local
alignments.
SYNOPSIS
localS db file2 match mismatch alpha beta [ flags ]
DESCRIPTION
localS finds the best local alignments between sequences in
db and the sequence in file2 (given a particular set of
scoring parameters), and reports those non-intersecting
local alignments having a score of at least a cutoff score
of # if the -c# option is specifi ed, or with # of non-
intersecting 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 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.
EXAMPLES
The examples below compare the sequence TAAAATAGAT with the
sequence TAGTAGATAGTAGAT, and demonstrate how different
choices for the scoring parameters can produce di ff erent
alignments. In both examples, only the best (i.e., highest
scoring) alignment is requested.
example% localS f1 f2 10 2 20 1 -n 1
finds 7 matches and 2 mismatches beginning at position 2 in the first sequence
and position 7 in the second sequence:
2 AAAATAGAT
| | |||||
7 ATAGTAGAT
for a score of 10(7) - 2(2) = 66.
example% localS f1 f2 10 2 2 1 -n 1
finds 10 matches, 3 one-letter indels and 1 two-letter indel beginning at
position 1 for both sequences:
1 TA--A-A-A-TAGAT
|| | | | |||||
1 TAGTAGATAGTAGAT
for a score of 10(10) - 3(2) - (2+1) = 91.
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), mlocalS(1), srlocalS(1), msrlocalS
(1),
trlocalS(1), mtrlocalS(1), pvlocalS(1), mpvlocalS(1
),
sequence-file(5)