View source for P53MH

[[Category:Software]][[Category:Biology]][[Category:Sequencing]]
{|<!--CONFIGURATION: REQUIRED-->
|{{#vardefine:app|p53mh}}
|{{#vardefine:url|http://www.jurgott.org/linkage/p53MH.htm}}
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|{{#vardefine:conf|}}           <!--CONFIGURATION-->
|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
|{{#vardefine:job|}}            <!--JOB SCRIPTS-->
|{{#vardefine:policy|}}         <!--POLICY-->
|{{#vardefine:testing|}}       <!--PROFILING-->
|{{#vardefine:faq|}}             <!--FAQ-->
|{{#vardefine:citation|1}}       <!--CITATION-->
|{{#vardefine:installation|}} <!--INSTALLATION-->
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<!--Description-->
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}

Computes a score between 0 and 100 for each site in the DNA sequence of a gene. A high score indicates an increased probability that n nucleotides at that and subsequent sites represent a p53 binding site, where n = 2 x 10 + (selected length of spacer region).

<!--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_{{uc:{{#var:app}}}}_BIN - executable directory
* HPC_{{uc:{{#var:app}}}}_DAT - example data directory
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{{#if: {{#var: conf}}|==Configuration==
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
|}}
<!--Run-->
{{#if: {{#var: exe}}|==Additional Information==

p53MH requires a data file. You can copy the example data file to your current working directory with the follow command:

 ml p53mh
 cp $HPC_P53MH_DAT/* .

|}}
<!--Job Scripts-->
{{#if: {{#var: job}}|==Job Script Examples==
See the [[{{PAGENAME}}_Job_Scripts]] page for {{#var: app}} Job script examples.
|}}
<!--Policy-->
{{#if: {{#var: policy}}|==Usage Policy==

WRITE USAGE POLICY HERE (Licensing, usage, access).

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<!--Performance-->
{{#if: {{#var: testing}}|==Performance==



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<!--Faq-->
{{#if: {{#var: faq}}|==FAQ==
*'''Q:''' **'''A:'''|}}
<!--Citation-->
{{#if: {{#var: citation}}|==Citation==
If you publish research that uses {{#var:app}} you have to cite it as follows:

[https://www.ncbi.nlm.nih.gov/pubmed/12077306 Hoh J, Jin S, Parrado T, Edington J, Levine AJ, Ott J (2002) The p53MH algorithm and its application in detecting p53-responsive genes. Proc Natl Acad Sci USA 99, 8467-8472]

|}}
<!--Installation-->
{{#if: {{#var: installation}}|==Installation==
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
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