{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T13:46:21Z","timestamp":1760708781527},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2016,11,3]],"date-time":"2016-11-03T00:00:00Z","timestamp":1478131200000},"content-version":"vor","delay-in-days":646,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: We present a novel method and corresponding application, MetAmp, to combine amplicon data from multiple genomic markers into Operational Taxonomic Units (OTUs) for microbial community analysis, calibrating the markers using data from known microbial genomes. When amplicons for multiple markers such as the 16S rRNA gene hypervariable regions are available, MetAmp improves the accuracy of OTU-based methods for characterizing bacterial composition and community structure. MetAmp works best with at least three markers, and is applicable to non-bacterial analyses and to non 16S markers. Our application and testing have been limited to 16S analysis of microbial communities.<\/jats:p>\n               <jats:p>Results: We clustered standard test sequences derived from the Human Microbiome Mock Community test sets and compared MetAmp and other tools with respect to their ability to recover OTUs for these benchmark bacterial communities. MetAmp compared favorably to QIIME, UPARSE and Mothur using amplicons from one, two, and three markers.<\/jats:p>\n               <jats:p>Availability and implementation: MetAmp is available at http:\/\/izhbannikov.github.io\/MetAmp\/<\/jats:p>\n               <jats:p>Contact: \u00a0ilyaz@uidaho.edu , foster@uidaho.edu<\/jats:p>\n               <jats:p>Supplementary information : Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv049","type":"journal-article","created":{"date-parts":[[2015,1,29]],"date-time":"2015-01-29T02:57:45Z","timestamp":1422500265000},"page":"1830-1832","source":"Crossref","is-referenced-by-count":8,"title":["MetAmp: combining amplicon data from multiple markers for OTU analysis"],"prefix":"10.1093","volume":"31","author":[{"given":"Ilya Y.","family":"Zhbannikov","sequence":"first","affiliation":[{"name":"1 Graduate Program in Bioinformatics and Computational Biology, University of Idaho and 2 Institute of Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID, USA"}]},{"given":"James A.","family":"Foster","sequence":"additional","affiliation":[{"name":"1 Graduate Program in Bioinformatics and Computational Biology, University of Idaho and 2 Institute of Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID, USA"},{"name":"1 Graduate Program in Bioinformatics and Computational Biology, University of Idaho and 2 Institute of Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID, USA"}]}],"member":"286","published-online":{"date-parts":[[2015,1,27]]},"reference":[{"key":"2023051505242097200_btv049-B1","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1038\/nmeth.2604","article-title":"Uparse: highly accurate otu sequences from microbial amplicon reads","volume":"10","author":"Edgar","year":"2013","journal-title":"Nat. Meth"},{"key":"2023051505242097200_btv049-B2","doi-asserted-by":"crossref","DOI":"10.1002\/0471250953.bi1007s36","article-title":"Using QIIME to analyze 16s rRNA gene sequences from microbial communities","author":"Kuczynski","year":"2011","journal-title":"Curr. Protoc. Bioinformatics"},{"key":"2023051505242097200_btv049-B3","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1109\/T-C.1969.222678","article-title":"A nonlinear mapping for data structure analysis","volume":"18","author":"Sammon","year":"1969","journal-title":"IEEE Trans. Comp."},{"key":"2023051505242097200_btv049-B4","doi-asserted-by":"crossref","first-page":"e27310","DOI":"10.1371\/journal.pone.0027310","article-title":"Reducing the effects of pcr amplification and sequencing artifacts on 16s rrna-based studies","volume":"6","author":"Schloss","year":"2011","journal-title":"PLoS One"},{"key":"2023051505242097200_btv049-B5","doi-asserted-by":"crossref","first-page":"977","DOI":"10.1016\/S0262-8856(03)00137-9","article-title":"Image registration methods: a survey","volume":"21","author":"Zitov","year":"2003","journal-title":"Image Vision Comput."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/11\/1830\/50314380\/bioinformatics_31_11_1830.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/11\/1830\/50314380\/bioinformatics_31_11_1830.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,15]],"date-time":"2023-05-15T05:25:14Z","timestamp":1684128314000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/11\/1830\/2365384"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,1,27]]},"references-count":5,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2015,6,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv049","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,6,1]]},"published":{"date-parts":[[2015,1,27]]}}}