{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T06:29:07Z","timestamp":1791872947497,"version":"4.3.4"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2016,11,10]],"date-time":"2016-11-10T00:00:00Z","timestamp":1478736000000},"content-version":"vor","delay-in-days":191,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Finding and translating stretches of DNA lacking stop codons is a task common in the analysis of sequence data. However, the computational tools for finding open reading frames are sufficiently slow that they are becoming a bottleneck as the volume of sequence data grows. This computational bottleneck is especially problematic in metagenomics when searching unassembled reads, or screening assembled contigs for genes of interest. Here, we present OrfM, a tool to rapidly identify open reading frames (ORFs) in sequence data by applying the Aho\u2013Corasick algorithm to find regions uninterrupted by stop codons. Benchmarking revealed that OrfM finds identical ORFs to similar tools (\u2018GetOrf\u2019 and \u2018Translate\u2019) but is four-five times faster. While OrfM is sequencing platform-agnostic, it is best suited to large, high quality datasets such as those produced by Illumina sequencers.<\/jats:p>\n               <jats:p>Availability and Implementation: Source code and binaries are freely available for download at http:\/\/github.com\/wwood\/OrfM or through GNU Guix under the LGPL 3+ license. OrfM is implemented in C and supported on GNU\/Linux and OSX.<\/jats:p>\n               <jats:p>Contacts: \u00a0b.woodcroft@uq.edu.au<\/jats:p>\n               <jats:p>Supplementary information : \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw241","type":"journal-article","created":{"date-parts":[[2016,5,4]],"date-time":"2016-05-04T01:03:16Z","timestamp":1462323796000},"page":"2702-2703","source":"Crossref","is-referenced-by-count":48,"title":["OrfM: a fast open reading frame predictor for metagenomic data"],"prefix":"10.1093","volume":"32","author":[{"given":"Ben J.","family":"Woodcroft","sequence":"first","affiliation":[{"name":"Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joel A.","family":"Boyd","sequence":"additional","affiliation":[{"name":"Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gene W.","family":"Tyson","sequence":"additional","affiliation":[{"name":"Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2016,5,3]]},"reference":[{"key":"2023020112585214700_btw241-B1","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1145\/360825.360855","article-title":"Efficient string matching: an aid to bibliographic search","volume":"18","author":"Aho","year":"1975","journal-title":"Communications of the ACM"},{"key":"2023020112585214700_btw241-B2","first-page":"183","article-title":"Metagenomics using next-generation sequencing","volume-title":"Methods Mol. 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Microbiol"},{"key":"2023020112585214700_btw241-B5","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1038\/nbt.2522","article-title":"Updating benchtop sequencing performance comparison","volume":"31","author":"J\u00fcnemann","year":"2013","journal-title":"Nat. Biotechnol"},{"key":"2023020112585214700_btw241-B6","doi-asserted-by":"crossref","first-page":"D115","DOI":"10.1093\/nar\/gkr1044","article-title":"IMG: the Integrated Microbial Genomes database and comparative analysis system","volume":"40","author":"Markowitz","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2023020112585214700_btw241-B7","doi-asserted-by":"crossref","first-page":"1882","DOI":"10.1111\/1462-2920.12086","article-title":"Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities","volume":"15","author":"Shakya","year":"2013","journal-title":"Environ. Microbiol"},{"key":"2023020112585214700_btw241-B8","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1126\/science.1107851","article-title":"Comparative metagenomics of microbial communities","volume":"308","author":"Tringe","year":"2005","journal-title":"Science"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/17\/2702\/49021108\/bioinformatics_32_17_2702.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/17\/2702\/49021108\/bioinformatics_32_17_2702.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T22:58:28Z","timestamp":1675292308000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/17\/2702\/2450737"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,5,3]]},"references-count":9,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2016,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw241","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2016,9,1]]},"published":{"date-parts":[[2016,5,3]]}}}