Difference between revisions of "HMMER"
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Revision as of 02:41, 10 August 2012
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.
Execution Environment and Modules
To use hmmer with the environment modules system at HPC the following commands are available:
Get module information for hmmer:
$module spider hmmer
Load the default application module:
$module load hmmer
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_HMMER_DIR - directory where hmmer is located.
- HPC_HMMER_BIN - executable directory