hmm2fetch1

Usage

Overview

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.