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ICHEC Software

Information about software packages installed on the ICHEC systems.

HMMER

Versions Installed

Fionn: 3.1b1

Description

HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called “profile hidden Markov models” (profile HMMs).

Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST.

License

HMMER is licensed under the GPLv3 (GNU General Public License, version 3).

Benchmarks

N/A.

Additional Notes

To use HMMER load the relevant environment module:

module load bio hmmer/intel/3.1b1

The HMMER package has been enabled with MPI, see below for an example PBS script. Further information can be obtained at http://hmmer.janelia.org/.

Job Submission Example

#!/bin/bash
#PBS -l nodes=1:ppn=24
#PBS -l walltime=00:10:00
#PBS -N MyJobName
#PBS -A MyProjectName
#PBS -j oe

module load bio hmmer/intel/3.1b1
cd $PBS_O_WORKDIR
module list

echo "Running test"
mpirun -n 2 hmmbuild SMC_N.hmm SMC_N.sto


exit 0

This job can be submitted using the command

qsub scriptname.pbs

Where scriptname.pbs is the filename of the sample PBS script

How to cite HMMER:

Durbin R., Eddy S., Krogh A. and Mitchison G. (1998)
Biological sequence analysis: probabilistic models of proteins and nucleic acids
Cambridge University Press.

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