RNAmmer: Difference between revisions

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Created page with "Category:Software {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|REPLACE}} |{{#vardefine:url|REPLACE}} <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> |{{#vardefin..."
 
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[[Category:Software]]
[[Category:Software]][[Category:Biology]][[Category:RNA-Seq]]
{|<!--CONFIGURATION: REQUIRED-->
{|<!--CONFIGURATION: REQUIRED-->
|{{#vardefine:app|REPLACE}}
|{{#vardefine:app|rnammer}}
|{{#vardefine:url|REPLACE}}
|{{#vardefine:url|http://www.cbs.dtu.dk/cgi-bin/nph-runsafe?man=rnammer}}
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
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|{{#vardefine:conf|}}          <!--CONFIGURATION-->
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<!--Modules-->
<!--Modules-->
==Required Modules==
==Environment Modules==
 
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
===Serial===
* {{#var:app}}
<!--
===Parallel (OpenMP)===
* intel
* {{#var:app}}
===Parallel (MPI)===
* intel
* openmpi
* {{#var:app}}
-->
==System Variables==
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
<!--Configuration-->
<!--Configuration-->
{{#if: {{#var: conf}}|==Configuration==
{{#if: {{#var: conf}}|==Configuration==

Latest revision as of 17:35, 10 June 2022

Description

rnammer website  

RNAmmer predicts ribosomal RNA genes in full genome sequences by util-ising two levels of Hidden Markov Models: An initial spotter model searches both strands. The spotter model is constructed from highly conserved loci within a structural alignment of known rRNA sequences. Once the spotter model detects an approximate position of a gene, flanking regions are extracted and parsed to the full model which matches the entire gene. By enabling a two-level approach it is avoided to run a full model through an entire genome sequence allowing faster predictions.

Environment Modules

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

System Variables

  • HPC_RNAMMER_DIR - installation directory




Citation

If you publish research that uses rnammer you have to cite it as follows:

Lagesen et al. 2007