论文信息 - Bioinformatics Applications Note Identification of Ribosomal Rna Genes in Metagenomic Fragments

Bioinformatics Applications Note Identification of Ribosomal Rna Genes in Metagenomic Fragments

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. Contact: liwz@sdsc.edu Supplementary information: Supplementary Data are available at Bioinformatics online.

[1] Irmtraud M. Meyer,et al. A practical guide to the art of RNA gene prediction , 2007, Briefings Bioinform..

[2] Guy Perrière,et al. The European ribosomal RNA database , 2004, Nucleic Acids Res..

[3] Edward M. Rubin,et al. Metagenomics: DNA sequencing of environmental samples , 2005, Nature Reviews Genetics.

[4] Sean R. Eddy,et al. Profile hidden Markov models , 1998, Bioinform..

[5] O. White,et al. Environmental Genome Shotgun Sequencing of the Sargasso Sea , 2004, Science.

[6] Peter F. Hallin,et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes , 2007, Nucleic acids research.

[7] P. Bork,et al. Get the most out of your metagenome: computational analysis of environmental sequence data. , 2007, Current opinion in microbiology.

[8] Jonathan P. Bollback,et al. Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. , 2006, Genome research.

[9] W. Ludwig,et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB , 2007, Nucleic acids research.

[10] Maciej Szymanski,et al. 5S Ribosomal RNA Database , 2002, Nucleic Acids Res..

[11] Maureen L. Coleman,et al. Microbial community gene expression in ocean surface waters , 2008, Proceedings of the National Academy of Sciences.