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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 & Restrictions

HMMER is available to all OSC users without restriction.

The following versions of HMMER are available on OSC systems:

Version Glenn Oakley
2.3.2 X  
3.0   X



To use HMMER on Glenn, first run the following commands:

module load biosoftw
module load hmmer

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: