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.
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).  
Hmmer programs may also be submitted to a queue using PBS script such as the one below:
#PBS -l nodes=1:ppn=8,pmem=1000mb,walltime=8:00:00
#PBS -m abe

module load hmmer
hmmbuild --cpu $PBS_NP globins4.hmm globins4.sto
hmmsearch --cpu $PBS_NP globins4.hmm globins45.fa > globins4.out
Note the use of --cpu $PBS_NP; this option is used to specify the number of threads used by Hmmer.
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.
Additional Information


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