Difference between revisions of "RepeatMasker"
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Moskalenko (talk | contribs) (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]] | [[Category:Software]][[Category:Bioinformatics]] | ||
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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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|{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | |{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | ||
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | ||
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{{#if: {{#var: url}}| | {{#if: {{#var: url}}| | ||
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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. | ||
| − | <!-- | + | <!--Modules--> |
| − | + | ==Environment Modules== | |
| − | == | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. |
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{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | ||
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{{#if: {{#var: pbs}}|==PBS Script Examples== | {{#if: {{#var: pbs}}|==PBS Script Examples== | ||
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | ||
| − | {{#if: {{#var: policy}}|==Usage | + | {{#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== | ||
Revision as of 17:27, 10 June 2022
Description
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