fitD
NAME
fitD - fit one sequence into another, reporting their dis-
tance
SYNOPSIS
fitD db file2 mismatch alpha beta [ flags ]
DESCRIPTION
fitD finds the best distance alignment between the sequences
in db and the sequence in file2, given a particular set of
scoring parameters.
The scoring parameters are all integer values, and all posi-
tive. The parameters mismatch, alpha and beta are added to
the score; match has a score of zero.
mismatch the amount to add for a mismatch.
alpha the amount to add for the first letter of an
insertion or deletion sequence (indel).
beta is the amount to add for subsequent letters in an
indel. For example, if there is a five-letter
indel, i.e. k = 5, then alpha + beta * ( k - 1 )
= alpha + beta * (4) will be added to 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.H. Sellers. "On the theory and computation of evolution-
ary distances". SIAM Journal of Applied Mathematics,
26 (1974) 787-793.
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), mfitD(1), f
itS(1), mfitS(1), pfitS(1),
sequence-file(5).