This is the Linux app named BIRAP whose latest release can be downloaded as Sample_Files.zip. It can be run online in the free hosting provider OnWorks for workstations.
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BIRAP
DESCRIPTION
BIRAP (Bacterial Intergenic Region Analysis Pipeline) is an open source, easy to use Perl pipeline that can be used to re-annotate bacterial genomes using experimental data. The tool integrates expression profile derived from RNA-seq and/or proteogenomics, compares it with existing in silico annotation and helps validate annotation, identify novel protein coding regions, putative non-coding RNA as well as help correct er-rors in the existing annotation. The pipeline requires “pileup” output from SAMtools for RNA-seq data and peptide/ePST locus file (GFF) from the Proteogenomic Mapping tool for prote-ogenomics data along with the genome and existing in silico annotation. When information regarding the locus of promot-ers and terminators in the genome (in .coords format) is pro-vided, the pipeline will also help identify non-coding RNA.
Features
- intergenic region analysis of bacterial genomes
- re-annotation of bacterial genomes
- small RNA (sRNA) detection
- RNA-seq
- Proteogenomics
Audience
Science/Research
User interface
Console/Terminal, Command-line
Programming Language
Perl
Categories
This is an application that can also be fetched from https://sourceforge.net/projects/birap/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.
