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.