{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T09:02:36Z","timestamp":1778058156966,"version":"3.51.4"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1454,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"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>Summary: Annotation of metagenomes involves comparing the individual sequence reads with a database of known sequences and assigning a unique function to each read. This is a time-consuming task that is computationally intensive (though not computationally complex). Here we present a novel approach to annotate metagenomes using unique k-mer oligopeptide sequences from 7 to 12 amino acids long. We demonstrate that k-mer-based annotations are faster and approach the sensitivity and precision of blastx-based annotations without loosing accuracy. A last-common ancestor approach was also developed to describe the members of the community.<\/jats:p>\n               <jats:p>Availability and implementation: This open-source application was implemented in Perl and can be accessed via a user-friendly website at http:\/\/edwards.sdsu.edu\/rtmg. In addition, code to access the annotation servers is available for download from http:\/\/www.theseed.org\/. FIGfams and k-mers are available for download from ftp:\/\/ftp.theseed.org\/FIGfams\/.<\/jats:p>\n               <jats:p>Contact: \u00a0redwards@mail.sdsu.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts599","type":"journal-article","created":{"date-parts":[[2012,10,10]],"date-time":"2012-10-10T08:45:27Z","timestamp":1349858727000},"page":"3316-3317","source":"Crossref","is-referenced-by-count":35,"title":["Real Time Metagenomics: Using <i>k<\/i>-mers to annotate metagenomes"],"prefix":"10.1093","volume":"28","author":[{"given":"Robert A.","family":"Edwards","sequence":"first","affiliation":[{"name":"1 Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, 2Department of Biology, 3Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, 4Computation Institute, University of Chicago, Chicago, IL 60637, USA and 5Fellowship for the Interpretation of Genomes, Burr Ridge, IL 60527, USA"},{"name":"1 Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, 2Department of Biology, 3Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, 4Computation Institute, University of Chicago, Chicago, IL 60637, USA and 5Fellowship for the Interpretation of Genomes, Burr Ridge, IL 60527, USA"},{"name":"1 Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, 2Department of Biology, 3Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, 4Computation Institute, University of Chicago, Chicago, IL 60637, USA and 5Fellowship for the Interpretation of Genomes, Burr Ridge, IL 60527, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert","family":"Olson","sequence":"additional","affiliation":[{"name":"1 Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, 2Department of Biology, 3Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, 4Computation Institute, University of Chicago, Chicago, IL 60637, USA and 5Fellowship for the Interpretation of Genomes, Burr Ridge, IL 60527, USA"},{"name":"1 Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, 2Department of Biology, 3Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, 4Computation Institute, University of Chicago, Chicago, IL 60637, USA and 5Fellowship for the Interpretation of Genomes, Burr Ridge, IL 60527, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Terry","family":"Disz","sequence":"additional","affiliation":[{"name":"1 Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, 2Department of Biology, 3Department of Computer Science, San Diego State 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Interpretation of Genomes, Burr Ridge, IL 60527, USA"},{"name":"1 Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, 2Department of Biology, 3Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, 4Computation Institute, University of Chicago, Chicago, IL 60637, USA and 5Fellowship for the Interpretation of Genomes, Burr Ridge, IL 60527, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Veronika","family":"Vonstein","sequence":"additional","affiliation":[{"name":"1 Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, 2Department of Biology, 3Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, 4Computation Institute, University of Chicago, Chicago, IL 60637, USA and 5Fellowship for the Interpretation of Genomes, Burr Ridge, IL 60527, 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