mfitD
NAME
mfitD - fit one sequence into another for minimum distance
using a penalty matrix
SYNOPSIS
mfitD db file2 matrix csub alpha beta [ flags ]
DESCRIPTION
mfitD reports the distance between the sequences in db and
the sequence in file2 (given a particular set of scoring
parameters), using a 26 by 26-letter penalty matrix.
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 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), fitD(1), fit
S(1), mfitS(1), pfitS(1),
penalty-matrix(5), sequence-file(5).