pfitS
NAME
pfitS - fit a profile sequence into an ordinary sequence.
SYNOPSIS
pfitS db profile match mismatch alpha beta [ flags ]
DESCRIPTION
pfitS finds the best alignment between the profile specified
in profile-file and the sequence in file.
profile the file containing profile information, where a
separate match score is assigned for each letter
in each position of a sequence. This differs from
the penalty matrix versions (see the matrix option
below), where one score is assigned to a given
letter match regardless of its position in the
sequence. Profile files have a suffix of ".pro";
they are specified without this extension (for
example, "globins.pro" is specified simply as
"globins"). For more information on the format of
a profile file, see profile(5).
The format of the sequence file db is our standard format,
the Pearson/FASTA format. The first line is the sequence
name, and should be used as a description. Subsequent lines
contain the sequence to be used. The sequences themselves
may contain blanks, returns, and other whitespace for reada-
bility. The sequence terminates at end-of-file, or if `>'
is read, beginning a new sequence in FASTA format. Multiple
sequences in this file will be processed.
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.
REFERENCES
P. Sellers. The theory and computation of evolutionary dis-
tances: pattern recognition. J. Algorithms, 1 (1980)
359-373.
M.S. Waterman and M. Perlwitz. "Line geometries for sequence
comparisons. Bull. Math. Biol., 1984. 46:567-77.
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), mglobalS(1), mglobalD(1), mfitS(1)
,
mfitD(1), moverS(1), mlocalS(1)
A>, msrlocalS(1), mtrlocalS(1),
mpvlocalS(1).