hmmer

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.


Info

Module Name

hmmer

Last Updated On

11/14/2023

Support Level

Secondary Support

Software Access Level

Open Access

Home Page

http://hmmer.janelia.org/

Documentation

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.

Agate Modules

Default

3.1b2_gcc-4.9.2_haswell

Other Modules

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

Mangi Modules

Default

3.3.2-openmpi-4.1.5-gcc-8.2.0-d5h5fvl

Other Modules

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

Mesabi Modules

Default

3.1b2_gcc-4.9.2_haswell

Other Modules

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