Identification and Removal of Ribosomal RNA Sequences from Metatranscriptomes

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2011 Dec 14

PMID 22155869

Citations 108

Authors

Robert Schmieder

Yan Wei Lim

Robert Edwards

Affiliations

Soon will be listed here.

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.

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