hmmer
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
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