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Bioinformatics. 2012 Feb 1;28(3):433-5. doi: 10.1093/bioinformatics/btr669. Epub 2011 Dec 6.

Identification and removal of ribosomal RNA sequences from metatranscriptomes.

Author information

1
Department of Computer Science, San Diego State University, San Diego, CA 92182, USA. rschmied@sciences.sdsu.edu

Abstract

SUMMARY:

Here, we present riboPicker, a robust framework for the rapid, automated identification and removal of ribosomal RNA sequences from metatranscriptomic datasets. The results can be exported for subsequent analysis, and the databases used for the web-based version are updated on a regular basis. riboPicker categorizes rRNA-like sequences and provides graphical visualizations and tabular outputs of ribosomal coverage, alignment results and taxonomic classifications.

AVAILABILITY AND IMPLEMENTATION:

This open-source application was implemented in Perl and can be used as stand-alone version or accessed online through a user-friendly web interface. The source code, user help and additional information is available at http://ribopicker.sourceforge.net/.

CONTACT:

rschmied@sciences.sdsu.edu; rschmied@sciences.sdsu.edu

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
22155869
PMCID:
PMC3268242
DOI:
10.1093/bioinformatics/btr669
[Indexed for MEDLINE]
Free PMC Article

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