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:
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:
A sample batch job is below:
#PBS -N hmmer #PBS -j oe #PBS -l nodes=1:ppn=1 #PBS -S /bin/bash cd $PBS_O_WORKDIR hmmalign globins4.align globins45 hmmbuild globins4.hmm globins4.align hmmsearch globins4.hmm /fdb/fastadb/nr.aa.fas > globins.out
- The HMMER home page
- The HMMER user group on Armstrong