man makemat (Commandes) - convert binary profiles into portable ASCII form

NAME

makemat - convert binary profiles into portable ASCII form

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.