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Bioinformatics Advance Access published online on April 3, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp161
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Identification of ribosomal RNA genes in metagenomic fragments

Ying Huang , Paul Gilna and Weizhong Li *

California Institute for Telecommunications and Information Technology, University of California San Diego, La Jolla, Cali-fornia, United States of America

*To whom correspondence should be addressed. Dr. Weizhong Li, E-mail: liwz{at}sdsc.edu


  Abstract

Motivation: Identification of genes coding for ribosomal RNA (rRNA) is considered an important goal in the analysis of data from metagenomics projects. Here we report the development of a soft-ware program designed for the identification of rRNA genes from metagenomic fragments based on hidden Markov models (HMMs). This program provides rRNA gene predictions with high sensitivity and specificity on artificially fragmented genomic DNAs.

Availability: Supplementary files, scripts and sample data are available at http://tools.camera.calit2.net/camera/meta_rna

Contact: liwz{at}sdsc.edu

Associate Editor: Prof. Ivo Hofacker

Received on November 3, 2008; revised on March 16, 2009; accepted on March 17, 2009

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