Difference between revisions of "PfamScan"

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[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]]
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[[Category:Software]][[Category:Biology]][[Category:Genomics]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|pfamscan}}
 
|{{#vardefine:app|pfamscan}}
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<!--Modules-->
 
<!--Modules-->
==Required Modules==
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==Environment Modules==
===Serial===
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
* {{#var:app}}
 
<!--
 
===Parallel (OpenMP)===
 
* intel
 
* {{#var:app}}
 
===Parallel (MPI)===
 
* intel
 
* openmpi
 
* {{#var:app}}
 
-->
 
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==
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On our system the pfamscan module is an alias for the [[HMMER3|hmmer]] module as we installed pfamscan within hmmer.
 
On our system the pfamscan module is an alias for the [[HMMER3|hmmer]] module as we installed pfamscan within hmmer.
  
You don't have to provide the '-dir' argument to the pfam_scan.pl command as we configured it to use the default location of the most current Pfam reference data release at '<code>/ufrc/data/reference/reference/pfam/current/</code>'.
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You don't have to provide the '-dir' argument to the pfam_scan.pl command as we configured it to use the default location of the most current Pfam reference data release at '<code>/data/reference/reference/pfam/current/</code>'.
  
 
|}}
 
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<!--Turn the Table of Contents and Edit paragraph links ON/OFF-->
 
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__NOTOC____NOEDITSECTION__
 
__NOTOC____NOEDITSECTION__
=Validation=
 
* Validated 4/5/2018
 

Latest revision as of 20:19, 12 August 2022

Description

pfamscan website  

Search a FASTA file against a library of Pfam HMMs

Environment Modules

Run module spider pfamscan to find out what environment modules are available for this application.

System Variables

  • HPC_PFAMSCAN_DIR - installation directory

Additional Information

On our system the pfamscan module is an alias for the hmmer module as we installed pfamscan within hmmer.

You don't have to provide the '-dir' argument to the pfam_scan.pl command as we configured it to use the default location of the most current Pfam reference data release at '/data/reference/reference/pfam/current/'.



Citation

If you publish research that uses pfamscan you have to cite it as follows:

The Pfam protein families database: R.D. Finn, A. Bateman, J. Clements, P. Coggill, R.Y. Eberhardt, S.R. Eddy, A. Heger, K. Hetherington, L. Holm, J. Mistry, E.L.L. Sonnhammer, J. Tate, M. Punta Nucleic Acids Research (2014) Database Issue 42:D222-D230