HMMER

Software Summary

Mesabi

Default Module:

3.1b2_gcc-4.9.2_haswell

Other Modules Available:

3.1b2_gcc-4.9.2_haswell, 3.3.2-openmpi-4.1.5-gcc-13.1.0-67byr44, 3.3.2-openmpi-4.1.5-gcc-8.2.0-d5h5fvl, 2.3.2, 3.0, 3.1-snap20121016, 3.1b2, 3.2.1

Last Updated On:

Tuesday, November 14, 2023

Mesabi K40

Default Module:

Other Modules Available:

Last Updated On:

Mangi

Default Module:

3.3.2-openmpi-4.1.5-gcc-8.2.0-d5h5fvl

Other Modules Available:

3.3.2-openmpi-4.1.5-gcc-13.1.0-67byr44, 3.3.2-openmpi-4.1.5-gcc-8.2.0-d5h5fvl, 2.3.2, 3.0, 3.1-snap20121016, 3.1b2, 3.2.1

Last Updated On:

Tuesday, November 14, 2023

Mangi v100

Default Module:

Other Modules Available:

Last Updated On:

NICE

Default Module:

Other Versions Available:

Last Updated On:

Tuesday, November 14, 2023

Support Level:

Secondary Support

Software Access Level:

Open Access

Home Page:

Link

Software Categories:

Biostatistics

Genetics

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.

Software Documentation

Software Documentation Tabs

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.

Additional Information

HMMER Documentation