Difference between revisions of "RepeatMasker"

From UFRC
Jump to navigation Jump to search
m (Text replace - "Usage policy" to "Usage Policy")
 
(10 intermediate revisions by 3 users not shown)
Line 1: Line 1:
 
__NOTOC__
 
__NOTOC__
 
__NOEDITSECTION__
 
__NOEDITSECTION__
−
[[Category:Software]][[Category:Bioinformatics]]
+
[[Category:Software]][[Category:Biology]]
−
<!-- ########  Template Configuration ######## -->
+
{|<!--Main settings - REQUIRED-->
−
<!--Edit definitions of the variables used in template calls
 
−
Required variables:
 
−
app - lowercase name of the application e.g. "amber"
 
−
url - url of the software page (project, company product, etc) - e.g. "http://ambermd.org/"
 
−
Optional variables:
 
−
INTEL - Version of the Intel Compiler e.g. "11.1"
 
−
MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
 
−
-->
 
−
{|
 
−
<!--Main settings - REQUIRED-->
 
 
|{{#vardefine:app|repeatmasker}}
 
|{{#vardefine:app|repeatmasker}}
 
|{{#vardefine:url|http://www.repeatmasker.org/}}
 
|{{#vardefine:url|http://www.repeatmasker.org/}}
−
<!--Compiler and MPI settings - OPTIONAL -->
 
−
|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
 
−
|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
 
−
<!--Choose sections to enable - OPTIONAL-->
 
−
|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
 
 
|{{#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-->
Line 42: Line 27:
 
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-->
−
==Available Versions==
+
==Environment Modules==
−
* 3.3.0
+
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
−
<!-- -->
+
==System Variables==
−
{{#if: {{#var: mod}}|==Execution Environment and Modules==
+
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
−
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
 
 
{{#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|}}

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




Retrieved from "https://help.rc.ufl.edu/mediawiki/index.php?title=RepeatMasker&oldid=24982"