Difference between revisions of "RepeatMasker"

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{|
 
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|{{#vardefine:app|repeatmasker}}
 
|{{#vardefine:app|repeatmasker}}
 
|{{#vardefine:url|http://www.repeatmasker.org/}}
 
|{{#vardefine:url|http://www.repeatmasker.org/}}
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<!--Description-->
 
<!--Description-->
 
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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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==Required Modules==
==Available Versions==
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[[Modules|modules documentation]]
* 3.3.0
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===Serial===
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*{{#var:app}}
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==System Variables==
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
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{{#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)|}}
 
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WRITE CITATION HERE
 
WRITE CITATION HERE
 
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=Validation=
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* Validated 4/5/2018

Latest revision as of 21:24, 6 December 2019

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.

Required Modules

modules documentation

Serial

  • repeatmasker

System Variables

  • HPC_REPEATMASKER_DIR - installation directory




Validation

  • Validated 4/5/2018