makemat (1)

makemat [\|-\|] [\|-E N\|] [\|-G N\|] [\|-H\|] [\|-P filename\|] [\|-S X\|] [\|-U str\|] [\|-d str\|] [\|-z N\|]

makemat converts a collection of binary profiles, created by the -C option of PSI-BLAST, into portable ASCII form.

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)

The National Center for Biotechnology Information.

blast(1), copymat(1), /usr/share/doc/blast2/impala.html