hmm2fetch(1) retrieve an HMM from an HMM database


hmm2fetch [options] database name


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.


Print brief help; includes version number and summary of all options, including expert options.

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.


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.


Sean Eddy
HHMI/Dept. of Genetics
Washington Univ. School of Medicine
4566 Scott Ave.
St Louis, MO 63110 USA