HMMer
Overview
HMMer is used to profile hidden Markov models.
Setup
To use HMMer it is necessary to set your HMMer environment by running a
special command sequence once per login session. You may optionally
place these commands in your .cshrc (C Shell users) or .profile (Bourne
Shell users) to avoid having to manually run these commands on login.
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For csh and tcsh:
source /usr/local/setup/hmmer.setup.csh
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For sh and bash:
. /usr/local/setup/hmmer.setup.sh
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Usage
HMMer contains several programs including:
hmmalign
- aligns sequences to an existing model
hmmbuild
- builds a model from a multiple sequence alignment
hmmcalibrate
- takes an HMM and empirically determines parameters
that are used to make searches more sensitive by
calculating more accurate expectation value scores
(E-values)
hmmconvert
- converts a model file into different formats, including
a compact HMMer 2 binary format and "best effort"
emulation of GCG profiles
hmmedit
- emits sequences probablistically from a profile HMM
hmmfetch
- gets a single model from an HMM database
hmmpfam
- searches an HMM database for matches to a query sequence
hmmsearch
- searches a sequence database for matches to an HMM.
afetch
- retrieves an alignment from an alignment database
alistat
- shows some simple statistics about a sequence alignment file
seqstat
- shows some simple statistics about a sequence file
sfetch
- retrieves a (sub-)sequence from a sequence file
shuffle
- randomizes sequences in a sequence file
sreformat
- reformats a sequence in a sequence file
Examples
The following is an example PBS script to run a hmmsearch on LION-XE for a
maximum of 2 hours to search for globin domains in the example Artemia
globin sequence in the sequence database Artemia.fa. Both the globin.hmm
file and the Artemia.fa file in this example are in /home/foo/hmmer. The
output will be in the standard PBS output file. This is an adaption of
part of the HMMer tutorial referred to in the Documentation section.
#PBS -l nodes=1:ppn=1
#PBS -l walltime=2:00:00
#PBS -j oe
#PBS -q lionxe-serial
# setup the HMMer environment
. /usr/local/setup/hmmer.setup.sh
# change the current working directory to the directory where
# the globin.hmm and the Artemia.fa files can be found
cd /home/foo/hmmer
# run the hmmer command
hmmsearch globin.hmm Artemia.fa
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Further information on PBS scripts and submitting jobs on the LION-XE cluster
can be found in the User Guides section of the HPC website.
Documentation
An excellent User Guide in PDF format can be found on LION-XE at
/usr/global/hmmer/Userguide.pdf that can be viewed with the command acroread.
HMMer command man pages can be accessed on LION-XE after
the setup script has been run.
Please send questions or suggestions about this web page to beatnic@aset.psu.edu
ASET | ITS | Penn State
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