NAME¶
- hmm2fetch - retrieve an HMM from an HMM database
-
SYNOPSIS¶
hmm2fetch [options] database name
DESCRIPTION¶
hmm2fetch is a small utility that retrieves an HMM called
name
from a HMMER model database called
database. in a new format, and
prints that model to standard output. For example,
hmm2fetch Pfam rrm
retrieves the RRM (RNA recognition motif) model from Pfam, if the environment
variable HMMERDB is set to the location of the Pfam database. The retrieved
HMM file is written in HMMER 2 ASCII format.
The database must have an associated GSI index file. To index an HMM database,
use the program
hmm2index.
OPTIONS¶
- -h
- Print brief help; includes version number and summary of all options,
including expert options.
- -n
- Interpret name as an HMM number instead of a name. Numbering starts
at 0. For example, to fetch the first HMM from an HMM database called
foo, you would do hmm2fetch -n 0 foo.
SEE ALSO¶
Master man page, with full list of and guide to the individual man pages: see
hmmer2(1).
For complete documentation, see the user guide
(
ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf); or see the
HMMER web page,
http://hmmer.janelia.org/.
COPYRIGHT¶
Copyright (C) 1992-2003 HHMI/Washington University School of Medicine.
Freely distributed under the GNU General Public License (GPL).
See the file COPYING in your distribution for details on redistribution
conditions.
AUTHOR¶
Sean Eddy
HHMI/Dept. of Genetics
Washington Univ. School of Medicine
4566 Scott Ave.
St Louis, MO 63110 USA
http://www.genetics.wustl.edu/eddy/