{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,19]],"date-time":"2026-06-19T07:40:57Z","timestamp":1781854857073,"version":"3.54.5"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"16","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Pyrosequencing technologies are frequently used for sequencing the 16S ribosomal RNA marker gene for profiling microbial communities. Clustering of the produced reads is an important but time-consuming task. We present Dynamic Seed-based Clustering (DySC), a new tool based on the greedy clustering approach that uses a dynamic seeding strategy. Evaluations based on the normalized mutual information (NMI) criterion show that DySC produces higher quality clusters than UCLUST and CD-HIT at a comparable runtime.<\/jats:p>\n               <jats:p>Availability and implementation: DySC, implemented in C, is available at http:\/\/code.google.com\/p\/dysc\/ under GNU GPL license.<\/jats:p>\n               <jats:p>Contact: \u00a0bertil.schmidt@uni-mainz.de<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts355","type":"journal-article","created":{"date-parts":[[2012,6,24]],"date-time":"2012-06-24T00:56:51Z","timestamp":1340499411000},"page":"2182-2183","source":"Crossref","is-referenced-by-count":19,"title":["DySC: software for greedy clustering of 16S rRNA reads"],"prefix":"10.1093","volume":"28","author":[{"given":"Zejun","family":"Zheng","sequence":"first","affiliation":[{"name":"Institut f\u00fcr Informatik, Johannes Gutenberg University Mainz, Mainz 55099, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan","family":"Kramer","sequence":"additional","affiliation":[{"name":"Institut f\u00fcr Informatik, Johannes Gutenberg University Mainz, Mainz 55099, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bertil","family":"Schmidt","sequence":"additional","affiliation":[{"name":"Institut f\u00fcr Informatik, Johannes Gutenberg University Mainz, Mainz 55099, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2012,6,23]]},"reference":[{"key":"2023012512531936800_B1","doi-asserted-by":"crossref","first-page":"e95","DOI":"10.1093\/nar\/gkr349","article-title":"ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time","volume":"39","author":"Cai","year":"2011","journal-title":"Nucleic Acid Res."},{"key":"2023012512531936800_B2","doi-asserted-by":"crossref","first-page":"D141","DOI":"10.1093\/nar\/gkn879","article-title":"The Ribosomal Database Project: improved alignments and new tools for rRNA analysis","volume":"37","author":"Cole","year":"2009","journal-title":"Nucleic Acid Res."},{"key":"2023012512531936800_B3","doi-asserted-by":"crossref","first-page":"2460","DOI":"10.1093\/bioinformatics\/btq461","article-title":"Search and clustering orders of magnitude faster than BLAST","volume":"26","author":"Edgar","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012512531936800_B4","doi-asserted-by":"crossref","first-page":"2194","DOI":"10.1093\/bioinformatics\/btr381","article-title":"UCHIME improves sensitivity and speed of chimera detection","volume":"27","author":"Edgar","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012512531936800_B5","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1093\/bioinformatics\/14.5.423","article-title":"Removing near-neighbour redundancy from large protein sequence collections","volume":"14","author":"Holm","year":"1998","journal-title":"Bioinformatics"},{"key":"2023012512531936800_B6","doi-asserted-by":"crossref","first-page":"1889","DOI":"10.1111\/j.1462-2920.2010.02193.x","article-title":"Ironing out the wrinkles in the rare biosphere through improved OTU clustering","volume":"12","author":"Huse","year":"2010","journal-title":"Environ. Microbiol."},{"key":"2023012512531936800_B7","doi-asserted-by":"crossref","first-page":"1658","DOI":"10.1093\/bioinformatics\/btl158","article-title":"Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences","volume":"22","author":"Li","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012512531936800_B8","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1093\/bioinformatics\/17.3.282","article-title":"Clustering of highly homologous sequences to reduce the size of large protein database","volume":"17","author":"Li","year":"2001","journal-title":"Bioinformatics"},{"key":"2023012512531936800_B9","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":"2023012512531936800_B10","doi-asserted-by":"crossref","first-page":"e8230","DOI":"10.1371\/journal.pone.0008230","article-title":"A high-throughput DNA sequence aligner for microbial ecology studies","volume":"4","author":"Schloss","year":"2009","journal-title":"PLoS One"},{"key":"2023012512531936800_B11","doi-asserted-by":"crossref","first-page":"e76","DOI":"10.1093\/nar\/gkp285","article-title":"ESPRIT: estimating species richness using large collections of 16S rDNA pyrosequences","volume":"37","author":"Sun","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012512531936800_B12","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1093\/bib\/bbr009","article-title":"A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis","volume":"13","author":"Sun","year":"2011","journal-title":"Brief Bioinform."},{"key":"2023012512531936800_B13","doi-asserted-by":"crossref","first-page":"480","DOI":"10.1038\/nature07540","article-title":"A core gut microbiome in obese and lean twins","volume":"457","author":"Turnbaugh","year":"2009","journal-title":"Nature"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/16\/2182\/48870672\/bioinformatics_28_16_2182.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/16\/2182\/48870672\/bioinformatics_28_16_2182.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T17:51:16Z","timestamp":1674669076000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/16\/2182\/325134"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,6,23]]},"references-count":13,"journal-issue":{"issue":"16","published-print":{"date-parts":[[2012,8,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts355","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,8,15]]},"published":{"date-parts":[[2012,6,23]]}}}