{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T06:25:54Z","timestamp":1768544754608,"version":"3.49.0"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2739,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Availability: Supplementary files, scripts and sample data are available at http:\/\/tools.camera.calit2.net\/camera\/meta_rna.<\/jats:p>\n               <jats:p>Contact: \u00a0liwz@sdsc.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary Data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp161","type":"journal-article","created":{"date-parts":[[2009,4,4]],"date-time":"2009-04-04T01:49:14Z","timestamp":1238809754000},"page":"1338-1340","source":"Crossref","is-referenced-by-count":192,"title":["Identification of ribosomal RNA genes in metagenomic fragments"],"prefix":"10.1093","volume":"25","author":[{"given":"Ying","family":"Huang","sequence":"first","affiliation":[{"name":"California Institute for Telecommunications and Information Technology, University of California, La Jolla, San Diego, California, USA"}]},{"given":"Paul","family":"Gilna","sequence":"additional","affiliation":[{"name":"California Institute for Telecommunications and Information Technology, University of California, La Jolla, San Diego, California, USA"}]},{"given":"Weizhong","family":"Li","sequence":"additional","affiliation":[{"name":"California Institute for Telecommunications and Information Technology, University of California, La Jolla, San Diego, California, USA"}]}],"member":"286","published-online":{"date-parts":[[2009,4,3]]},"reference":[{"key":"2023013110290994600_B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023013110290994600_B2","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1093\/bioinformatics\/14.9.755","article-title":"Profile hidden Markov models","volume":"14","author":"Eddy","year":"1998","journal-title":"Bioinformatics"},{"key":"2023013110290994600_B3","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1101\/gr.5890907","article-title":"Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA","volume":"17","author":"Freyhult","year":"2007","journal-title":"Genome Res."},{"key":"2023013110290994600_B4","doi-asserted-by":"crossref","first-page":"3805","DOI":"10.1073\/pnas.0708897105","article-title":"Microbial community gene expression in ocean surface waters","volume":"105","author":"Frias-Lopez","year":"2008","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023013110290994600_B5","doi-asserted-by":"crossref","first-page":"3100","DOI":"10.1093\/nar\/gkm160","article-title":"RNAmmer: consistent and rapid annotation of ribosomal RNA genes","volume":"35","author":"Lagesen","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023013110290994600_B6","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1093\/bib\/bbm011","article-title":"A practical guide to the art of RNA gene prediction","volume":"8","author":"Meyer","year":"2007","journal-title":"Brief. Bioinform."},{"key":"2023013110290994600_B7","doi-asserted-by":"crossref","first-page":"490","DOI":"10.1016\/j.mib.2007.09.001","article-title":"Get the most out of your metagenome: computational analysis of environmental sequence data","volume":"10","author":"Raes","year":"2007","journal-title":"Curr. Opin. Microbiol."},{"key":"2023013110290994600_B8","doi-asserted-by":"crossref","first-page":"7188","DOI":"10.1093\/nar\/gkm864","article-title":"SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB","volume":"35","author":"Pruesse","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023013110290994600_B9","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1093\/nar\/30.1.176","article-title":"5S Ribosomal RNA database","volume":"30","author":"Szymanski","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"2023013110290994600_B10","doi-asserted-by":"crossref","first-page":"805","DOI":"10.1038\/nrg1709","article-title":"Metagenomics: DNA sequencing of environmental samples","volume":"6","author":"Tringe","year":"2005","journal-title":"Nat. Rev. Genet."},{"key":"2023013110290994600_B11","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1126\/science.1093857","article-title":"Environmental genome shotgun sequencing of the Sargasso Sea","volume":"304","author":"Venter","year":"2004","journal-title":"Science"},{"key":"2023013110290994600_B12","doi-asserted-by":"crossref","first-page":"D101","DOI":"10.1093\/nar\/gkh065","article-title":"The European ribosomal RNA database","volume":"32","author":"Wuyts","year":"2004","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/10\/1338\/48986752\/bioinformatics_25_10_1338.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/10\/1338\/48986752\/bioinformatics_25_10_1338.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T20:37:43Z","timestamp":1675197463000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/10\/1338\/270806"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,4,3]]},"references-count":12,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2009,5,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp161","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,5,15]]},"published":{"date-parts":[[2009,4,3]]}}}