{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T00:07:06Z","timestamp":1775002026779,"version":"3.50.1"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":480,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Metagenomic data, which contains sequenced DNA reads of uncultured microbial species from environmental samples, provide a unique opportunity to thoroughly analyze microbial species that have never been identified before. Reconstructing 16S ribosomal RNA, a phylogenetic marker gene, is usually required to analyze the composition of the metagenomic data. However, massive volume of dataset, high sequence similarity between related species, skewed microbial abundance and lack of reference genes make 16S rRNA reconstruction difficult. Generic de novo assembly tools are not optimized for assembling 16S rRNA genes. In this work, we introduce a targeted rRNA assembly tool, REAGO (REconstruct 16S ribosomal RNA Genes from metagenOmic data). It addresses the above challenges by combining secondary structure-aware homology search, zproperties of rRNA genes and de novo assembly. Our experimental results show that our tool can correctly recover more rRNA genes than several popular generic metagenomic assembly tools and specially designed rRNA construction tools.<\/jats:p>\n               <jats:p>Availability and implementation: The source code of REAGO is freely available at https:\/\/github.com\/chengyuan\/reago.<\/jats:p>\n               <jats:p>Contact: \u00a0yannisun@msu.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv231","type":"journal-article","created":{"date-parts":[[2015,6,13]],"date-time":"2015-06-13T17:12:36Z","timestamp":1434215556000},"page":"i35-i43","source":"Crossref","is-referenced-by-count":151,"title":["Reconstructing 16S rRNA genes in metagenomic data"],"prefix":"10.1093","volume":"31","author":[{"given":"Cheng","family":"Yuan","sequence":"first","affiliation":[{"name":"1 Computer Science and Engineering, Michigan State Univerisity, 428 South Shaw Rd East Lansing, MI 48824, USA and 2Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jikai","family":"Lei","sequence":"additional","affiliation":[{"name":"1 Computer Science and Engineering, Michigan State Univerisity, 428 South Shaw Rd East Lansing, MI 48824, USA and 2Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James","family":"Cole","sequence":"additional","affiliation":[{"name":"1 Computer Science and Engineering, Michigan State Univerisity, 428 South Shaw Rd East Lansing, MI 48824, USA and 2Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yanni","family":"Sun","sequence":"additional","affiliation":[{"name":"1 Computer Science and Engineering, Michigan State Univerisity, 428 South Shaw Rd East Lansing, MI 48824, USA and 2Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,6,10]]},"reference":[{"key":"2023020115395721700_btv231-B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"2023020115395721700_btv231-B2","doi-asserted-by":"crossref","first-page":"D46","DOI":"10.1093\/nar\/gkp1024","article-title":"GenBank","volume":"38","author":"Benson","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023020115395721700_btv231-B3","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1016\/0966-842X(96)10057-3","article-title":"The indigenous gastrointestinal microflora","volume":"4","author":"Berg","year":"1996","journal-title":"Trends Microbiol."},{"key":"2023020115395721700_btv231-B4","doi-asserted-by":"crossref","first-page":"810","DOI":"10.1101\/gr.7337908","article-title":"ALLPATHS: de novo assembly of whole-genome shotgun microreads","volume":"18","author":"Butler","year":"2008","journal-title":"Genome Res."},{"key":"2023020115395721700_btv231-B5","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1264\/jsme2.ME08525","article-title":"Global sequencing: a review of current molecular data and new methods available to assess microbial diversity","volume":"23","author":"Christen","year":"2008","journal-title":"Microbes Environ. JSME"},{"key":"2023020115395721700_btv231-B6","doi-asserted-by":"crossref","first-page":"D19","DOI":"10.1093\/nar\/gkn765","article-title":"Petabyte-scale innovations at the European nucleotide archive","volume":"37","author":"Cochrane","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023020115395721700_btv231-B7","doi-asserted-by":"crossref","first-page":"D294","DOI":"10.1093\/nar\/gki038","article-title":"The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis","volume":"33","author":"Cole","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023020115395721700_btv231-B8","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511790492","volume-title":"Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids","author":"Durbin","year":"1998"},{"key":"2023020115395721700_btv231-B9","doi-asserted-by":"crossref","first-page":"e39948","DOI":"10.1371\/journal.pone.0039948","article-title":"Reconstruction of ribosomal RNA genes from metagenomic data","volume":"7","author":"Fan","year":"2012","journal-title":"PloS One"},{"key":"2023020115395721700_btv231-B10","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1186\/1471-2105-13-82","article-title":"Readjoiner: a fast and memory efficient string graph-based sequence assembler","volume":"13","author":"Gonnella","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"2023020115395721700_btv231-B11","doi-asserted-by":"crossref","first-page":"1141","DOI":"10.1101\/gr.085464.108","article-title":"Microbial community profiling for human microbiome projects: tools, techniques, and challenges","volume":"19","author":"Hamady","year":"2009","journal-title":"Genome Res."},{"key":"2023020115395721700_btv231-B12","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1038\/nrg3068","article-title":"Next-generation transcriptome assembly","volume":"12","author":"Jeffrey","year":"2011","journal-title":"Nat. Rev. Genet."},{"key":"2023020115395721700_btv231-B13","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1093\/bioinformatics\/btp154","article-title":"Local RNA structure alignment with incomplete sequence","volume":"25","author":"Kolbe","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020115395721700_btv231-B14","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1023\/A:1020573408652","article-title":"The cell membrane plays a crucial role in survival of bacteria and archaea in extreme environments","volume":"81","author":"Konings","year":"2002","journal-title":"Antonie Van Leeuwenhoek"},{"key":"2023020115395721700_btv231-B15","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1089\/cmb.2010.0244","article-title":"Genovo: de novo assembly for metagenomes","volume":"18","author":"Laserson","year":"2011","journal-title":"J. Comput. Biol."},{"key":"2023020115395721700_btv231-B16","article-title":"WGSIM-read simulator for next generation sequencing","author":"Li","year":"2011"},{"key":"2023020115395721700_btv231-B17","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1101\/gr.097261.109","article-title":"De novo assembly of human genomes with massively parallel short read sequencing","volume":"20","author":"Li","year":"2010","journal-title":"Genome Res."},{"key":"2023020115395721700_btv231-B18","doi-asserted-by":"crossref","first-page":"804","DOI":"10.1126\/science.1064088","article-title":"Biodiversity and ecosystem functioning: current knowledge and future challenges","volume":"294","author":"Loreau","year":"2001","journal-title":"Science"},{"key":"2023020115395721700_btv231-B19","doi-asserted-by":"crossref","first-page":"898","DOI":"10.1038\/ismej.2011.147","article-title":"Individual genome assembly from complex community short-read metagenomic datasets","volume":"6","author":"Luo","year":"2012","journal-title":"ISME J."},{"key":"2023020115395721700_btv231-B20","doi-asserted-by":"crossref","first-page":"R44","DOI":"10.1186\/gb-2011-12-5-r44","article-title":"EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data","volume":"12","author":"Miller","year":"2011","journal-title":"Genome Biol."},{"key":"2023020115395721700_btv231-B21","doi-asserted-by":"crossref","first-page":"e155","DOI":"10.1093\/nar\/gks678","article-title":"MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads","volume":"40","author":"Namiki","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023020115395721700_btv231-B22","doi-asserted-by":"crossref","first-page":"1335","DOI":"10.1093\/bioinformatics\/btp157","article-title":"Infernal 1.0: inference of RNA alignments","volume":"25","author":"Nawrocki","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020115395721700_btv231-B23","doi-asserted-by":"crossref","first-page":"i94","DOI":"10.1093\/bioinformatics\/btr216","article-title":"Meta-IDBA: a de novo assembler for metagenomic data","volume":"27","author":"Peng","year":"2011","journal-title":"Bioinformatics"},{"key":"2023020115395721700_btv231-B24","doi-asserted-by":"crossref","first-page":"1420","DOI":"10.1093\/bioinformatics\/bts174","article-title":"IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth","volume":"28","author":"Peng","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020115395721700_btv231-B25","doi-asserted-by":"crossref","first-page":"1092","DOI":"10.1038\/35059215","article-title":"Life in extreme environments","volume":"409","author":"Rothschild","year":"2001","journal-title":"Nature"},{"key":"2023020115395721700_btv231-B26","doi-asserted-by":"crossref","first-page":"e1000186","DOI":"10.1371\/journal.pcbi.1000186","article-title":"Gene-boosted assembly of a novel bacterial genome from very short reads","volume":"4","author":"Salzberg","year":"2008","journal-title":"PLOS Comput. Biol."},{"key":"2023020115395721700_btv231-B27","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1146\/annurev.mi.31.100177.000543","article-title":"Microbial ecology of the gastrointestinal tract","volume":"31","author":"Savage","year":"1977","journal-title":"Annu. Rev. Microbiol."},{"key":"2023020115395721700_btv231-B28","doi-asserted-by":"crossref","first-page":"1882","DOI":"10.1111\/1462-2920.12086","article-title":"Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities","volume":"15","author":"Shakya","year":"2013","journal-title":"Environ. Microbiol."},{"key":"2023020115395721700_btv231-B29","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1101\/gr.126953.111","article-title":"Efficient de novo assembly of large genomes using compressed data structures","volume":"22","author":"Simpson","year":"2012","journal-title":"Genome Res."},{"key":"2023020115395721700_btv231-B30","doi-asserted-by":"crossref","first-page":"1117","DOI":"10.1101\/gr.089532.108","article-title":"ABySS: a parallel assembler for short read sequence data","volume":"19","author":"Simpson","year":"2009","journal-title":"Genome Res."},{"key":"2023020115395721700_btv231-B31","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/30.1.27","article-title":"DNA Data Bank of Japan (DDBJ) for genome scale research in life science","volume":"30","author":"Tateno","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"2023020115395721700_btv231-B32","doi-asserted-by":"crossref","first-page":"R2","DOI":"10.1186\/gb-2013-14-1-r2","article-title":"MetAMOS: a modular and open source metagenomic assembly and analysis pipeline","volume":"14","author":"Treangen","year":"2013","journal-title":"Genome Biol."},{"key":"2023020115395721700_btv231-B33","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1126\/science.1107851","article-title":"Comparative metagenomics of microbial communities","volume":"308","author":"Tringe","year":"2005","journal-title":"Science"},{"key":"2023020115395721700_btv231-B34","doi-asserted-by":"crossref","first-page":"5261","DOI":"10.1128\/AEM.00062-07","article-title":"Nave Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy","volume":"73","author":"Wang","year":"2007","journal-title":"Appl. Environ. Microbiol."},{"key":"2023020115395721700_btv231-B35","doi-asserted-by":"crossref","first-page":"5088","DOI":"10.1073\/pnas.74.11.5088","article-title":"Phylogenetic structure of the prokaryotic domain: the primary kingdoms","volume":"74","author":"Woese","year":"1977","journal-title":"Proc. Natl. Acad. Sci."},{"key":"2023020115395721700_btv231-B36","doi-asserted-by":"crossref","first-page":"4576","DOI":"10.1073\/pnas.87.12.4576","article-title":"Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya","volume":"87","author":"Woese","year":"1990","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2023020115395721700_btv231-B37","doi-asserted-by":"crossref","first-page":"i363","DOI":"10.1093\/bioinformatics\/bts388","article-title":"Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics","volume":"28","author":"Wu","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020115395721700_btv231-B38","doi-asserted-by":"crossref","first-page":"e77596","DOI":"10.1371\/journal.pone.0077596","article-title":"RNA-CODE: A noncoding RNA classification tool for short reads in NGS data lacking reference genomes","volume":"8","author":"Yuan","year":"2013","journal-title":"PLoS One"},{"key":"2023020115395721700_btv231-B39","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1101\/gr.074492.107","article-title":"Velvet: algorithms for de novo short read assembly using de Bruijn graphs","volume":"18","author":"Zerbino","year":"2008","journal-title":"Genome Res."},{"key":"2023020115395721700_btv231-B40","doi-asserted-by":"crossref","first-page":"e1003737","DOI":"10.1371\/journal.pcbi.1003737","article-title":"A scalable and accurate targeted gene assembly tool (SAT-assembler) for next-generation sequencing data","volume":"10","author":"Zhang","year":"2014","journal-title":"PLoS Comput. Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/12\/i35\/49013221\/bioinformatics_31_12_i35.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/12\/i35\/49013221\/bioinformatics_31_12_i35.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T00:05:34Z","timestamp":1675296334000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/12\/i35\/215357"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,6,10]]},"references-count":40,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2015,6,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv231","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,6,15]]},"published":{"date-parts":[[2015,6,10]]}}}