Difference between revisions of "RepeatMasker"

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(Created page with "__NOTOC__ __NOEDITSECTION__ Category:SoftwareCategory:Bioinformatics <!-- ######## Template Configuration ######## --> <!--Edit definitions of the variables used in temp...")
 
 
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[[Category:Software]][[Category:Bioinformatics]]
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[[Category:Software]][[Category:Biology]]
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{|
 
<!--Main settings - REQUIRED-->
 
 
|{{#vardefine:app|repeatmasker}}
 
|{{#vardefine:app|repeatmasker}}
 
|{{#vardefine:url|http://www.repeatmasker.org/}}
 
|{{#vardefine:url|http://www.repeatmasker.org/}}
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<!--Description-->
 
<!--Description-->
 
{{#if: {{#var: url}}|
 
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
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RepeatMasker is a program that screens DNA sequences for interspersed
 
RepeatMasker is a program that screens DNA sequences for interspersed
 
repeats and low complexity DNA sequences. The output of the program is
 
repeats and low complexity DNA sequences. The output of the program is
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performed by one of several popular search engines including,
 
performed by one of several popular search engines including,
 
cross_match, ABBlast/WUBlast, RMBlast and Decypher.
 
cross_match, ABBlast/WUBlast, RMBlast and Decypher.
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==Environment Modules==
==Available Versions==
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
* 3.3.0
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==System Variables==
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
{{#if: {{#var: mod}}|==Running the application using modules==
 
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{{#if: {{#var: exe}}|==How To Run==
 
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WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
 
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{{#if: {{#var: pbs}}|==PBS Script Examples==
 
{{#if: {{#var: pbs}}|==PBS Script Examples==
 
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See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
{{#if: {{#var: policy}}|==Usage policy==
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{{#if: {{#var: policy}}|==Usage Policy==
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 
{{#if: {{#var: testing}}|==Performance==
 
{{#if: {{#var: testing}}|==Performance==

Latest revision as of 20:32, 12 August 2022

Description

repeatmasker website  

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). On average, almost 50% of a human genomic DNA sequence currently will be masked by the program. Sequence comparisons in RepeatMasker are performed by one of several popular search engines including, cross_match, ABBlast/WUBlast, RMBlast and Decypher.

Environment Modules

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

System Variables

  • HPC_REPEATMASKER_DIR - installation directory