NAME
makemat - convert binary profiles into portable ASCII form
SYNOPSIS
makemat [-] [-E N] [-G N] [-H] [-P filename] [-S X] [-U str] [-d str] [-z N]
DESCRIPTION
makemat converts a collection of binary profiles, created by the -C option of PSI-BLAST, into portable ASCII form.
OPTIONS
A summary of options is included below.
- -
-
Print usage message
- -E N
-
Cost to extend a gap (default = 1)
- -G N
-
Cost to open a gap (default = 11)
- -H
-
Print help; overrides all other arguments
- -P filename
-
Database name for profile database (default = stdin)
- -S X
-
Scaling factor for matrix outputs to avoid round-off problems (default = 100)
- -U str
-
Underlying Matrix (default = BLOSUM62)
- -d str
-
Underlying sequence database used to make profiles (default = nr)
- -z N
-
Effective length of the profile database (0 for length of -d option)
AUTHOR
The National Center for Biotechnology Information.
SEE ALSO
blast(1), copymat(1), /usr/share/doc/blast2/impala.html