{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,4]],"date-time":"2026-04-04T05:42:22Z","timestamp":1775281342827,"version":"3.50.1"},"reference-count":22,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2017,5,10]],"date-time":"2017-05-10T00:00:00Z","timestamp":1494374400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2017,5,10]],"date-time":"2017-05-10T00:00:00Z","timestamp":1494374400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1R01AI116706-01A1"],"award-info":[{"award-number":["1R01AI116706-01A1"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1P20DK108268"],"award-info":[{"award-number":["1P20DK108268"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U01HL121831"],"award-info":[{"award-number":["U01HL121831"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2017,12]]},"DOI":"10.1186\/s12859-017-1670-4","type":"journal-article","created":{"date-parts":[[2017,5,10]],"date-time":"2017-05-10T02:31:00Z","timestamp":1494383460000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":196,"title":["A Bayesian taxonomic classification method for 16S rRNA gene sequences with improved species-level accuracy"],"prefix":"10.1186","volume":"18","author":[{"given":"Xiang","family":"Gao","sequence":"first","affiliation":[]},{"given":"Huaiying","family":"Lin","sequence":"additional","affiliation":[]},{"given":"Kashi","family":"Revanna","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4610-1670","authenticated-orcid":false,"given":"Qunfeng","family":"Dong","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2017,5,10]]},"reference":[{"issue":"Suppl 8","key":"1670_CR1","doi-asserted-by":"crossref","first-page":"S17","DOI":"10.1186\/1471-2164-13-S8-S17","volume":"13","author":"JM Fettweis","year":"2012","unstructured":"Fettweis JM, Serrano MG, Sheth NU, et al. Species-level classification of the vaginal microbiome. BMC Genomics. 2012;13 Suppl 8:S17.","journal-title":"BMC Genomics"},{"issue":"16","key":"1670_CR2","doi-asserted-by":"publisher","first-page":"5261","DOI":"10.1128\/AEM.00062-07","volume":"73","author":"Q Wang","year":"2007","unstructured":"Wang Q, Garrity GM, Tiedje JM, et al. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007;73(16):5261\u20137.","journal-title":"Appl Environ Microbiol"},{"issue":"2","key":"1670_CR3","doi-asserted-by":"publisher","first-page":"e0116106","DOI":"10.1371\/journal.pone.0116106","volume":"10","author":"N Chaudhary","year":"2015","unstructured":"Chaudhary N, Sharma AK, Agarwal P, et al. 16S classifier: a tool for fast and accurate taxonomic classification of 16S rRNA hypervariable regions in metagenomic datasets. PLoS One. 2015;10(2):e0116106.","journal-title":"PLoS One"},{"issue":"1","key":"1670_CR4","doi-asserted-by":"publisher","first-page":"324","DOI":"10.1186\/s12859-015-0747-1","volume":"16","author":"G Allard","year":"2015","unstructured":"Allard G, Ryan FJ, Jeffery IB, et al. SPINGO: a rapid species-classifier for microbial amplicon sequences. BMC Bioinformatics. 2015;16(1):324.","journal-title":"BMC Bioinformatics"},{"issue":"5","key":"1670_CR5","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1038\/nmeth.f.303","volume":"7","author":"JG Caporaso","year":"2010","unstructured":"Caporaso JG, Kuczynski J, Stombaugh J, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7(5):335\u20136.","journal-title":"Nat Methods"},{"issue":"1","key":"1670_CR6","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-9-1","volume":"9","author":"F Meyer","year":"2008","unstructured":"Meyer F, Paarmann D, D\u2019Souza M, et al. The metagenomics RAST server\u2013a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics. 2008;9(1):1.","journal-title":"BMC Bioinformatics"},{"key":"1670_CR7","doi-asserted-by":"crossref","unstructured":"Vilo C, Dong Q. Evaluation of the RDP classifier accuracy using 16S rRNA gene variable regions. Metagenomics. 2012;1:1\u20135.","DOI":"10.4303\/mg\/235551"},{"issue":"6","key":"1670_CR8","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1007\/s002390010184","volume":"52","author":"LB Koski","year":"2001","unstructured":"Koski LB, Golding GB. The closest BLAST hit is often not the nearest neighbor. J Mol Evol. 2001;52(6):540\u20132.","journal-title":"J Mol Evol"},{"issue":"3","key":"1670_CR9","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1101\/gr.5969107","volume":"17","author":"DH Huson","year":"2007","unstructured":"Huson DH, Auch AF, Qi J, et al. MEGAN analysis of metagenomic data. Genome Res. 2007;17(3):377\u201386.","journal-title":"Genome Res"},{"issue":"17","key":"1670_CR10","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"SF Altschul","year":"1997","unstructured":"Altschul SF, Madden TL, Schaffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25(17):3389\u2013402.","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"1670_CR11","doi-asserted-by":"publisher","first-page":"5069","DOI":"10.1128\/AEM.03006-05","volume":"72","author":"TZ DeSantis","year":"2006","unstructured":"DeSantis TZ, Hugenholtz P, Larsen N, et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006;72(7):5069\u201372.","journal-title":"Appl Environ Microbiol"},{"issue":"5","key":"1670_CR12","doi-asserted-by":"publisher","first-page":"1792","DOI":"10.1093\/nar\/gkh340","volume":"32","author":"RC Edgar","year":"2004","unstructured":"Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792\u20137.","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"1670_CR13","doi-asserted-by":"publisher","first-page":"783","DOI":"10.2307\/2408678","volume":"39","author":"J Felsenstein","year":"1985","unstructured":"Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 1985;39(4):783\u201391.","journal-title":"Evolution"},{"issue":"1","key":"1670_CR14","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2164-13-341","volume":"13","author":"MA Quail","year":"2012","unstructured":"Quail MA, Smith M, Coupland P, et al. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics. 2012;13(1):1.","journal-title":"BMC Genomics"},{"issue":"3","key":"1670_CR15","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/gb-2014-15-3-r46","volume":"15","author":"DE Wood","year":"2014","unstructured":"Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 2014;15(3):1\u201312.","journal-title":"Genome Biol"},{"key":"1670_CR16","volume-title":"Evaluation: from precision, recall and F-measure to ROC, informedness, markedness and correlation","author":"DM Powers","year":"2011","unstructured":"Powers DM. Evaluation: from precision, recall and F-measure to ROC, informedness, markedness and correlation. 2011."},{"issue":"6","key":"1670_CR17","doi-asserted-by":"publisher","first-page":"R76","DOI":"10.1186\/gb-2014-15-6-r76","volume":"15","author":"M Pop","year":"2014","unstructured":"Pop M, Walker AW, Paulson J, et al. Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition. Genome Biol. 2014;15(6):R76.","journal-title":"Genome Biol"},{"issue":"10","key":"1670_CR18","doi-asserted-by":"publisher","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","volume":"5","author":"RC Gentleman","year":"2004","unstructured":"Gentleman RC, Carey VJ, Bates DM, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004;5(10):R80.","journal-title":"Genome Biol"},{"issue":"Database issue","key":"1670_CR19","doi-asserted-by":"publisher","first-page":"D294","DOI":"10.1093\/nar\/gki038","volume":"33","author":"JR Cole","year":"2005","unstructured":"Cole JR, Chai B, Farris RJ, et al. The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res. 2005;33(Database issue):D294\u20136.","journal-title":"Nucleic Acids Res"},{"key":"1670_CR20","doi-asserted-by":"publisher","first-page":"19233","DOI":"10.1038\/srep19233","volume":"6","author":"S Lindgreen","year":"2016","unstructured":"Lindgreen S, Adair KL, Gardner PP. An evaluation of the accuracy and speed of metagenome analysis tools. Sci Rep. 2016;6:19233.","journal-title":"Sci Rep"},{"key":"1670_CR21","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1016\/j.mimet.2016.01.011","volume":"122","author":"F Valenzuela-Gonz\u00e1lez","year":"2016","unstructured":"Valenzuela-Gonz\u00e1lez F, Mart\u00ednez-Porchas M, Villalpando-Canchola E, et al. Studying long 16S rDNA sequences with ultrafast-metagenomic sequence classification using exact alignments (Kraken). J Microbiol Methods. 2016;122:38\u201342.","journal-title":"J Microbiol Methods"},{"key":"1670_CR22","doi-asserted-by":"crossref","DOI":"10.1201\/9780429246593","volume-title":"An introduction to the bootstrap","author":"B Efron","year":"1994","unstructured":"Efron B, Tibshirani RJ. An introduction to the bootstrap. Boca Raton: CRC press; 1994."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-017-1670-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-017-1670-4\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-017-1670-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,14]],"date-time":"2020-05-14T10:44:47Z","timestamp":1589453087000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-017-1670-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,5,10]]},"references-count":22,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2017,12]]}},"alternative-id":["1670"],"URL":"https:\/\/doi.org\/10.1186\/s12859-017-1670-4","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,5,10]]},"assertion":[{"value":"18 January 2017","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 May 2017","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"10 May 2017","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"247"}}