{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,16]],"date-time":"2026-04-16T16:30:30Z","timestamp":1776357030723,"version":"3.51.2"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"24","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The application of next-generation sequencing (NGS) technologies to RNAs directly extracted from a community of organisms yields a mixture of fragments characterizing both coding and non-coding types of RNAs. The task to distinguish among these and to further categorize the families of messenger RNAs and ribosomal RNAs (rRNAs) is an important step for examining gene expression patterns of an interactive environment and the phylogenetic classification of the constituting species.<\/jats:p>\n               <jats:p>Results: We present SortMeRNA, a new software designed to rapidly filter rRNA fragments from metatranscriptomic data. It is capable of handling large sets of reads and sorting out all fragments matching to the rRNA database with high sensitivity and low running time.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/bioinfo.lifl.fr\/RNA\/sortmerna<\/jats:p>\n               <jats:p>Contact: \u00a0evguenia.kopylova@lifl.fr<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts611","type":"journal-article","created":{"date-parts":[[2012,10,16]],"date-time":"2012-10-16T03:56:11Z","timestamp":1350359771000},"page":"3211-3217","source":"Crossref","is-referenced-by-count":2789,"title":["SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data"],"prefix":"10.1093","volume":"28","author":[{"given":"Evguenia","family":"Kopylova","sequence":"first","affiliation":[{"name":"1 LIFL (UMR CNRS 8022 Universit\u00e9 Lille 1) and 2Inria Lille Nord-Europe, 59655 Villeneuve d'Ascq, France"},{"name":"1 LIFL (UMR CNRS 8022 Universit\u00e9 Lille 1) and 2Inria Lille Nord-Europe, 59655 Villeneuve d'Ascq, France"}]},{"given":"Laurent","family":"No\u00e9","sequence":"additional","affiliation":[{"name":"1 LIFL (UMR CNRS 8022 Universit\u00e9 Lille 1) and 2Inria Lille Nord-Europe, 59655 Villeneuve d'Ascq, France"},{"name":"1 LIFL (UMR CNRS 8022 Universit\u00e9 Lille 1) and 2Inria Lille Nord-Europe, 59655 Villeneuve d'Ascq, France"}]},{"given":"H\u00e9l\u00e8ne","family":"Touzet","sequence":"additional","affiliation":[{"name":"1 LIFL (UMR CNRS 8022 Universit\u00e9 Lille 1) and 2Inria Lille Nord-Europe, 59655 Villeneuve d'Ascq, France"},{"name":"1 LIFL (UMR CNRS 8022 Universit\u00e9 Lille 1) and 2Inria Lille Nord-Europe, 59655 Villeneuve d'Ascq, France"}]}],"member":"286","published-online":{"date-parts":[[2012,10,15]]},"reference":[{"key":"2023012513253841500_bts611-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. 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