hmmer

Summary

• Module Name: hmmer

• Support Level: Secondary Support

• Software Access Level: Open Access

• Home Page: http://hmmer.janelia.org/

Software Description

HMMER is an implementation of profile hidden Markov model (HMM) methods for sensitive database searches using multiple sequence alignments as queries. HMMER takes a multiple sequence alignment as input. It can then build a statistical model called a “hidden Markov model” which can be used as a query into a sequence database to find (and/or align) additional homologues of the sequence family.

General Linux

To run this software interactively in a Linux environment run the commands:

module load hmmer
hmmbuild [-options] hmmout.file align.file

This will build a profile HMM (hmmout.file) from an input alignment file (align.file). For a complete list of options, use the -h option, e.g.,

hmmbuild -h

Other programs available in HMMER are:

• phmmer - Search a sequence against a sequence database.

• jackhmmer - Iteratively search a sequence against a sequence database.

• hmmbuild - Build a profile HMM from an input multiple alignment.

• hmmsearch - Search a profile HMM against a sequence database.

• hmmscan - Search a sequence against a profile HMM database.

• hmmalign - Make a multiple alignment of many sequences to a common profile HMM.

• hmmconvert - Convert profile formats to/from HMMER3 format.

• hmmemit - Generate sequences from a profile HMM.

• hmmfetch - Get a profile HMM by name or accession from an HMM database.

• hmmpress - Format an HMM database into a binary format for hmmscan.

• hmmstat - Show summary statistics for each profile in an HMM database.

For instructions on how to use each of these, use the -h option in the command line or visit the HMMER homepage.