Profile hidden Markov models (profile HMMs) can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus. HMMER uses profile HMMs, and can be useful in situations like:

  • if you are working with an evolutionarily diverse protein family, a BLAST search with any individual sequence may not find the rest of the sequences in the family.
  • the top hits in a BLAST search are hypothetical sequences from genome projects.
  • your protein consists of several domains which are of different types.

HMMER (pronounced 'hammer', as in a more precise mining tool than BLAST) was developed by Sean Eddy at Washington University in St. Louis.

HMMER is a very cpu-intensive program and is parallelized using threads, so that each instance of hmmsearch or the other search programs can use all the cpus available on a node. HMMER on OSC clusters are intended for those who need to run HMMER searches on large numbers of query sequences.

Availability and Restrictions


The following versions of HMMER are available on OSC systems:

Version Oakley
3.0 X*
* Current default version

You can use module spider hmmer to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.


HMMER is available to all OSC users without restriction.

Publisher/Vendor/Repository and License Type, Open source (academic)



To use HMMER on Oakley, first run the following command:

module load hmmer


Once the hmmer module is loaded, the following commands will be available for your use:

Single sequence queries: new to HMMER3
phmmer Search a sequence against a sequence database. (BLASTP-like)
jackhmmer Iteratively search a sequence against a sequence database. (PSIBLAST-like)

Replacements for HMMER2’s functionality
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.

Other utilities
hmmconvert Convert profile formats to/from HMMER3 format.
hmmemit Generate (sample) 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.

If you need to know options for a command, type the command name followed by "-h", for example:

hmmalign -h 

Batch Usage

A sample batch job is below:

#PBS -N hmmer
#PBS -j oe
#PBS -l nodes=1:ppn=1
#PBS -S /bin/bash

hmmalign globins4.align globins45
hmmbuild globins4.hmm globins4.align
hmmsearch globins4.hmm /fdb/fastadb/nr.aa.fas > globins.out

Further Reading

See Also

Fields of Science: