Information about software packages installed on the ICHEC systems.
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.
HMMER is licensed under the GPLv3 (GNU General Public License, version 3).
To use HMMER load the relevant environment module:
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
#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
echo "Running test"
mpirun -n 2 hmmbuild SMC_N.hmm SMC_N.sto
This job can be submitted using the command
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.