Difference between revisions of "Barrnap"

From UFRC
Jump to navigation Jump to search
(Created page with "Category:SoftwareCategory:BiologyCategory:RNA-Seq {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|barrnap}} |{{#vardefine:url|http://www.vicbioinformatics.com/s...")
 
m (Text replacement - "#uppercase" to "uc")
 
Line 37: Line 37:
 
-->
 
-->
 
==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 21:06, 6 December 2019

Description

barrnap website  

Barrnap predicts the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).

It takes FASTA DNA sequence as input, and write GFF3 as output. It uses the new NHMMER tool that comes with HMMER 3.1 for HMM searching in RNA:DNA style. NHMMER binaries for 64-bit Linux and Mac OS X are included and will be auto-detected. Multithreading is supported and one can expect roughly linear speed-ups with more CPUs. Running time is approximately 1 second per 1 megabase of input sequence.

Required Modules

Serial

  • barrnap

System Variables

  • HPC_BARRNAP_DIR - installation directory