Identification of ribosomal RNA genes in metagenomic fragments

Ying Huang; Paul Gilna; Weizhong Li

doi:10.1093/bioinformatics/btp161

Identification of ribosomal RNA genes in metagenomic fragments

Bioinformatics. 2009 May 15;25(10):1338-40. doi: 10.1093/bioinformatics/btp161. Epub 2009 Apr 3.

Authors

Ying Huang¹, Paul Gilna, Weizhong Li

Affiliation

¹ California Institute for Telecommunications and Information Technology, University of California, La Jolla, San Diego, California, USA.

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 software 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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Genes, rRNA / genetics*
Genomics / methods*
Software*