Difference between revisions of "PolyPHen"

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(Created page with "Category:SoftwareCategory:BiologyCategory:Genomics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|REPLACE}} |{{#vardefine:url|REPLACE}} <!--CONFIGURATION: OPTI...")
 
 
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[[Category:Software]][[Category:Biology]][[Category:Genomics]]
 
[[Category:Software]][[Category:Biology]][[Category:Genomics]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
|{{#vardefine:app|REPLACE}}
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|{{#vardefine:app|polyphen}}
|{{#vardefine:url|REPLACE}}
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|{{#vardefine:url|http://genetics.bwh.harvard.edu/pph2/dokuwiki/overview}}
 
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<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 
|{{#vardefine:conf|}}          <!--CONFIGURATION-->
 
|{{#vardefine:conf|}}          <!--CONFIGURATION-->
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|{{#vardefine:testing|}}      <!--PROFILING-->
 
|{{#vardefine:testing|}}      <!--PROFILING-->
 
|{{#vardefine:faq|}}            <!--FAQ-->
 
|{{#vardefine:faq|}}            <!--FAQ-->
|{{#vardefine:citation|}}      <!--CITATION-->
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|{{#vardefine:citation|1}}      <!--CITATION-->
 
|{{#vardefine:installation|}} <!--INSTALLATION-->
 
|{{#vardefine:installation|}} <!--INSTALLATION-->
 
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
 
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_{{#uppercase:{{#var:app}}}}_BIN - executable directory
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* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
  
 
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If you publish research that uses {{#var:app}} you have to cite it as follows:
 
If you publish research that uses {{#var:app}} you have to cite it as follows:
  
WRITE_CITATION_HERE
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[http://www.ncbi.nlm.nih.gov/pubmed/20354512 Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. Nat Methods 7(4):248-249 (2010).]
  
 
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Latest revision as of 18:45, 27 May 2022

Description

polyphen website  

PolyPhen-2 (Polymorphism Phenotyping v2) is a software tool which predicts possible impact of amino acid substitutions on the structure and function of human proteins using straightforward physical and evolutionary comparative considerations.

Environment Modules

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

System Variables

  • HPC_POLYPHEN_DIR - installation directory
  • HPC_POLYPHEN_BIN - executable directory




Citation

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

Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. Nat Methods 7(4):248-249 (2010).