{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,22]],"date-time":"2026-02-22T02:54:13Z","timestamp":1771728853033,"version":"3.50.1"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1762,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Here, we present riboPicker, a robust framework for the rapid, automated identification and removal of ribosomal RNA sequences from metatranscriptomic datasets. The results can be exported for subsequent analysis, and the databases used for the web-based version are updated on a regular basis. riboPicker categorizes rRNA-like sequences and provides graphical visualizations and tabular outputs of ribosomal coverage, alignment results and taxonomic classifications.<\/jats:p>\n               <jats:p>Availability and implementation: This open-source application was implemented in Perl and can be used as stand-alone version or accessed online through a user-friendly web interface. The source code, user help and additional information is available at http:\/\/ribopicker.sourceforge.net\/.<\/jats:p>\n               <jats:p>Contact: \u00a0rschmied@sciences.sdsu.edu; rschmied@sciences.sdsu.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr669","type":"journal-article","created":{"date-parts":[[2011,12,8]],"date-time":"2011-12-08T01:24:20Z","timestamp":1323307460000},"page":"433-435","source":"Crossref","is-referenced-by-count":186,"title":["Identification and removal of ribosomal RNA sequences from metatranscriptomes"],"prefix":"10.1093","volume":"28","author":[{"given":"Robert","family":"Schmieder","sequence":"first","affiliation":[{"name":"1 Department of Computer Science 2Computational Science Research Center 3Department of Biology, San Diego State University, San Diego, CA 92182 and 4Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA"},{"name":"1 Department of Computer Science 2Computational Science Research Center 3Department of Biology, San Diego State University, San Diego, CA 92182 and 4Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA"}]},{"given":"Yan Wei","family":"Lim","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science 2Computational Science Research Center 3Department of Biology, San Diego State University, San Diego, CA 92182 and 4Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA"}]},{"given":"Robert","family":"Edwards","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science 2Computational Science Research Center 3Department of Biology, San Diego State University, San Diego, CA 92182 and 4Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA"},{"name":"1 Department of Computer Science 2Computational Science Research Center 3Department of Biology, San Diego State University, San Diego, CA 92182 and 4Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA"}]}],"member":"286","published-online":{"date-parts":[[2011,12,6]]},"reference":[{"key":"2023012512165809100_B1","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1186\/1471-2164-9-75","article-title":"The RAST Server: Rapid Annotations using Subsystems Technology","volume":"9","author":"Aziz","year":"2008","journal-title":"BMC Genomics"},{"key":"2023012512165809100_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 Acids Res."},{"key":"2023012512165809100_B3","doi-asserted-by":"crossref","first-page":"5069","DOI":"10.1128\/AEM.03006-05","article-title":"Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB","volume":"72","author":"DeSantis","year":"2006","journal-title":"Appl. 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