hmmpress

Langue: en

Version: 371450 (fedora - 01/12/10)

Section: 1 (Commandes utilisateur)

Sommaire

NAME

hmmpress - prepare an HMM database for hmmscan

SYNOPSIS

hmmpress [options] <hmmfile>

DESCRIPTION

Starting from a profile database <hmmfile> in standard HMMER3 format, construct binary compressed datafiles for hmmscan. The hmmpress step is required for hmmscan to work.

Four files are created: <hmmfile>.h3m, <hmmfile>.h3i, <hmmfile>.h3f, and <hmmfile>.h3p. The <hmmfile>.h3m file contains the profile HMMs and their annotation in a binary format. The <hmmfile>.h3i file is an SSI index for the <hmmfile>.h3m file. The <hmmfile>.h3f file contains precomputed data structures for the fast heuristic filter (the MSV filter). The <hmmfile>.h3p file contains precomputed data structures for the rest of each profile.

OPTIONS

-h
Help; print a brief reminder of command line usage and all available options.
-f
Force; overwrites any previous hmmpress'ed datafiles. The default is to bitch about any existing files and ask you to delete them first.

SEE ALSO

See hmmer(1) for a master man page with a list of all the individual man pages for programs in the HMMER package.

For complete documentation, see the user guide that came with your HMMER distribution (Userguide.pdf); or see the HMMER web page (@HMMER_URL@).

 @HMMER_COPYRIGHT@
 @HMMER_LICENSE@

For additional information on copyright and licensing, see the file called COPYRIGHT in your HMMER source distribution, or see the HMMER web page (@HMMER_URL@).

AUTHOR

 Eddy/Rivas Laboratory
 Janelia Farm Research Campus
 19700 Helix Drive
 Ashburn VA 20147 USA
 http://eddylab.org