HMMER is a collection of programs which implement a Hidden Markov Model
sequence homology search.
HMMER searches sequence databases for sequence homologs, and for
information necessary to create sequence alignments. It uses
probabilistic models called profile hidden Markov models.
HMMER is often used with a profile database, such as Pfam
or many of the databases that participate in Interpro. HMMER includes
programs that can also work with query sequences, not just profiles,
just like BLAST. For example, you can search a protein query sequence
against a database with phmmer, or do an iterative search with jackhmmer.
HMMER is designed to detect remote homologs as sensitively as possible,
relying on the strength of its underlying probability models. In the past,
this strength came at significant computational expense, but as of the
new HMMER3 project, HMMER is now essentially as fast as BLAST.
The HMMER home page at hmmer.org:
Sean Eddy, Travis Wheeler, HMMER Development Team,
HMMER User's Guide,
Biological sequence analysis using profile hidden Markov models,
On any ARC cluster, check the installation details
by typing "module spider hmmer".
HMMER requires that the appropriate modules be loaded before it can be used.
One version of the appropriate commands for use on NewRiver is:
module purge module load gcc/5.2.0 module load openmpi/1.8.5 module load hmmer/3.1b2
The following batch file runs HMMER, building a profile and
then searching a sequence database.
#! /bin/bash # #PBS -l walltime=0:05:00 #PBS -l nodes=1:ppn=1 #PBS -W group_list=newriver #PBS -q open_q #PBS -j oe # cd $PBS_O_WORKDIR # module purge module load gcc/5.2.0 module load openmpi/1.8.5 module load hmmer/3.1b2 # hmmbuild globins4.hmm globins4.sto # hmmsearch globins4.hmm globins45.fa
A complete set of files to carry out a similar process are available in