View source for HMMER

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[[Category:Software]][[Category:Biology]][[Category:Genomics]]
{|<!--Main settings - REQUIRED-->
|{{#vardefine:app|hmmer}}
|{{#vardefine:url|http://hmmer.janelia.org/}}
|{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
|{{#vardefine:pbs|}} <!--Enable PBS script wiki page link-->
|{{#vardefine:policy|}} <!--Enable policy section -->
|{{#vardefine:testing|}} <!--Enable performance testing/profiling section -->
|{{#vardefine:faq|}} <!--Enable FAQ section -->
|{{#vardefine:citation|}} <!--Enable Reference/Citation section -->
|}
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<!--Description-->
{{#if: {{#var: url}}|
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}

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.
<!--Modules-->
==Environment Modules==
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
==System Variables==
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_HMMER_BIN - executable directory
{{#if: {{#var: exe}}|==Additional Information==
phmmer and hmmsearch only work with fasta formatted target sequence databases. We provide the following fasta formatted databases either downloaded or extracted from the BLAST databases:
* [http://www.uniprot.org/ UniProt] - /project/bio/fasta/uniprot/uniprot_sprot.fasta
* [http://www.ncbi.nlm.nih.gov/protein NCBI NR] - /project/bio/fasta/nr/nr.fa
* [http://www.ncbi.nlm.nih.gov/protein NCBI RefSeq] - /project/bio/fasta/refseq/refseq_protein.fa
|}}
{{#if: {{#var: conf}}|==Configuration==
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
{{#if: {{#var: pbs}}|==PBS Script Examples==
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
{{#if: {{#var: policy}}|==Usage Policy==
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
{{#if: {{#var: testing}}|==Performance==
WRITE PERFORMANCE TESTING RESULTS HERE|}}
{{#if: {{#var: faq}}|==FAQ==
*'''Q:''' **'''A:'''|}}
{{#if: {{#var: citation}}|==Citation==
If you publish research that uses {{{app}}} you have to cite it as follows:
WRITE CITATION HERE
|}}