Difference between revisions of "PolyPHen"
Jump to navigation
Jump to search
(Created page with "Category:SoftwareCategory:BiologyCategory:Genomics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|REPLACE}} |{{#vardefine:url|REPLACE}} <!--CONFIGURATION: OPTI...") |
|||
| (2 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
[[Category:Software]][[Category:Biology]][[Category:Genomics]] | [[Category:Software]][[Category:Biology]][[Category:Genomics]] | ||
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
| − | |{{#vardefine:app| | + | |{{#vardefine:app|polyphen}} |
| − | |{{#vardefine:url| | + | |{{#vardefine:url|http://genetics.bwh.harvard.edu/pph2/dokuwiki/overview}} |
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
| Line 10: | Line 10: | ||
|{{#vardefine:testing|}} <!--PROFILING--> | |{{#vardefine:testing|}} <!--PROFILING--> | ||
|{{#vardefine:faq|}} <!--FAQ--> | |{{#vardefine:faq|}} <!--FAQ--> | ||
| − | |{{#vardefine:citation|}} <!--CITATION--> | + | |{{#vardefine:citation|1}} <!--CITATION--> |
|{{#vardefine:installation|}} <!--INSTALLATION--> | |{{#vardefine:installation|}} <!--INSTALLATION--> | ||
|} | |} | ||
| Line 25: | Line 25: | ||
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_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory |
<!--Configuration--> | <!--Configuration--> | ||
| Line 61: | Line 61: | ||
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: | ||
| − | + | [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).] | |
|}} | |}} | ||
Latest revision as of 18:45, 27 May 2022
Description
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: