Difference between revisions of "HMMER"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) m (Text replace - "<!--Compiler and MPI settings - OPTIONAL --> |{" to "|{") |
Moskalenko (talk | contribs) |
||
| Line 27: | Line 27: | ||
strength came at significant computational expense, but in the new HMMER3 | strength came at significant computational expense, but in the new HMMER3 | ||
project, HMMER is now essentially as fast as BLAST. | project, HMMER is now essentially as fast as BLAST. | ||
| − | |||
<!--Modules--> | <!--Modules--> | ||
==Required Modules== | ==Required Modules== | ||
| Line 33: | Line 32: | ||
===Serial=== | ===Serial=== | ||
*{{#var:app}} | *{{#var:app}} | ||
| + | ==System Variables== | ||
| + | * HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory | ||
* HPC_HMMER_BIN - executable directory | * HPC_HMMER_BIN - executable directory | ||
{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
Revision as of 18:49, 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.
Required Modules
Serial
- hmmer
System Variables
- HPC_{{#uppercase:hmmer}}_DIR - installation directory
- HPC_HMMER_BIN - executable directory