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.
<hmmfile> may not be '-' (dash); running
hmmpress on a
standard input stream rather than a file is not allowed.
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 ().
COPYRIGHT¶
Copyright (C) 2013 Howard Hughes Medical Institute.
Freely distributed under the GNU General Public License (GPLv3).
For additional information on copyright and licensing, see the file called
COPYRIGHT in your HMMER source distribution, or see the HMMER web page ().
AUTHOR¶
Eddy/Rivas Laboratory
Janelia Farm Research Campus
19700 Helix Drive
Ashburn VA 20147 USA
http://eddylab.org