fitS
NAME
fitS - fit one sequence into another.
SYNOPSIS
fitS db file2 match mismatch alpha beta [ flags ]
DESCRIPTION
fitS finds the best similarity alignment between the
sequences in db and the sequence in file2, given a particu-
lar set of scoring parameters.
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.
REFERENCES
P. Sellers. The theory and computation of evolutionary dis-
tances: pattern recognition. J. Algorithms, 1 (1980)
359-373.
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), mfitS(1),
pfitS(1), fitD(1), mfitD(1),
sequence-file(5).