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 Marko...

Descripción completa

Detalles Bibliográficos
Autores principales: Huang, Ying, Gilna, Paul, Li, Weizhong
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2009
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2677747/
https://www.ncbi.nlm.nih.gov/pubmed/19346323
http://dx.doi.org/10.1093/bioinformatics/btp161
_version_ 1782166796723290112
author Huang, Ying
Gilna, Paul
Li, Weizhong
author_facet Huang, Ying
Gilna, Paul
Li, Weizhong
author_sort Huang, Ying
collection PubMed
description 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.
format Text
id pubmed-2677747
institution National Center for Biotechnology Information
language English
publishDate 2009
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-26777472009-05-08 Identification of ribosomal RNA genes in metagenomic fragments Huang, Ying Gilna, Paul Li, Weizhong Bioinformatics Applications Note 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. Oxford University Press 2009-05-15 2009-04-03 /pmc/articles/PMC2677747/ /pubmed/19346323 http://dx.doi.org/10.1093/bioinformatics/btp161 Text en © 2009 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ 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.
spellingShingle Applications Note
Huang, Ying
Gilna, Paul
Li, Weizhong
Identification of ribosomal RNA genes in metagenomic fragments
title Identification of ribosomal RNA genes in metagenomic fragments
title_full Identification of ribosomal RNA genes in metagenomic fragments
title_fullStr Identification of ribosomal RNA genes in metagenomic fragments
title_full_unstemmed Identification of ribosomal RNA genes in metagenomic fragments
title_short Identification of ribosomal RNA genes in metagenomic fragments
title_sort identification of ribosomal rna genes in metagenomic fragments
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2677747/
https://www.ncbi.nlm.nih.gov/pubmed/19346323
http://dx.doi.org/10.1093/bioinformatics/btp161
work_keys_str_mv AT huangying identificationofribosomalrnagenesinmetagenomicfragments
AT gilnapaul identificationofribosomalrnagenesinmetagenomicfragments
AT liweizhong identificationofribosomalrnagenesinmetagenomicfragments

Ejemplares similares