{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T11:09:23Z","timestamp":1790766563132,"version":"4.1.0"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1008727","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,3,10]],"date-time":"2021-03-10T00:00:00Z","timestamp":1615334400000}}],"reference-count":27,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2021,2,26]],"date-time":"2021-02-26T00:00:00Z","timestamp":1614297600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R35\u2013GM130151"],"award-info":[{"award-number":["R35\u2013GM130151"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01-HG006677"],"award-info":[{"award-number":["R01-HG006677"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    Low-cost, high-throughput sequencing has led to an enormous increase in the number of sequenced microbial genomes, with well over 100,000 genomes in public archives today. Automatic genome annotation tools are integral to understanding these organisms, yet older gene finding methods must be retrained on each new genome. We have developed a universal model of prokaryotic genes by fitting a temporal convolutional network to amino-acid sequences from a large, diverse set of microbial genomes. We incorporated the new model into a gene finding system, Balrog (Bacterial Annotation by Learned Representation Of Genes), which does not require genome-specific training and which matches or outperforms other state-of-the-art gene finding tools. Balrog is freely available under the MIT license at\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/salzberg-lab\/Balrog\" xlink:type=\"simple\">https:\/\/github.com\/salzberg-lab\/Balrog<\/jats:ext-link>\n                    .\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1008727","type":"journal-article","created":{"date-parts":[[2021,2,26]],"date-time":"2021-02-26T13:41:26Z","timestamp":1614346886000},"page":"e1008727","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":35,"title":["Balrog: A universal protein model for prokaryotic gene prediction"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3414-1875","authenticated-orcid":true,"given":"Markus J.","family":"Sommer","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven L.","family":"Salzberg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2021,2,26]]},"reference":[{"issue":"2","key":"pcbi.1008727.ref001","doi-asserted-by":"crossref","first-page":"544","DOI":"10.1093\/nar\/26.2.544","article-title":"Microbial gene identification using interpolated Markov models","volume":"26","author":"SL Salzberg","year":"1998","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"pcbi.1008727.ref002","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1093\/bioinformatics\/btm009","article-title":"Identifying bacterial genes and endosymbiont DNA with Glimmer","volume":"23","author":"AL Delcher","year":"2007","journal-title":"Bioinformatics"},{"issue":"4","key":"pcbi.1008727.ref003","doi-asserted-by":"crossref","first-page":"1107","DOI":"10.1093\/nar\/26.4.1107","article-title":"GeneMark.hmm: new solutions for gene finding","volume":"26","author":"AV Lukashin","year":"1998","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"pcbi.1008727.ref004","doi-asserted-by":"crossref","first-page":"1079","DOI":"10.1101\/gr.230615.117","article-title":"Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes","volume":"28","author":"A Lomsadze","year":"2018","journal-title":"Genome Res"},{"key":"pcbi.1008727.ref005","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1186\/1471-2105-11-119","article-title":"Prodigal: prokaryotic gene recognition and translation initiation site identification","volume":"11","author":"D Hyatt","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"pcbi.1008727.ref006","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1007\/978-1-4939-6622-6_11","article-title":"Finding Genes in Genome Sequence","volume":"1525","author":"AC McHardy","year":"2017","journal-title":"Methods Mol Biol"},{"issue":"9","key":"pcbi.1008727.ref007","doi-asserted-by":"crossref","first-page":"e43176","DOI":"10.1371\/journal.pone.0043176","article-title":"Theoretical prediction and experimental verification of protein-coding genes in plant pathogen genome Agrobacterium tumefaciens strain C58","volume":"7","author":"Q Wang","year":"2012","journal-title":"PLoS One"},{"issue":"14","key":"pcbi.1008727.ref008","doi-asserted-by":"crossref","first-page":"6614","DOI":"10.1093\/nar\/gkw569","article-title":"NCBI prokaryotic genome annotation pipeline","volume":"44","author":"T Tatusova","year":"2016","journal-title":"Nucleic acids research"},{"issue":"D1","key":"pcbi.1008727.ref009","first-page":"D570","article-title":"MGnify: the microbiome analysis resource in 2020","volume":"48","author":"AL Mitchell","year":"2020","journal-title":"Nucleic Acids Res"},{"issue":"14","key":"pcbi.1008727.ref010","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"T Seemann","year":"2014","journal-title":"Bioinformatics"},{"issue":"D1","key":"pcbi.1008727.ref011","doi-asserted-by":"crossref","first-page":"D851","DOI":"10.1093\/nar\/gkx1068","article-title":"RefSeq: an update on prokaryotic genome annotation and curation","volume":"46","author":"DH Haft","year":"2018","journal-title":"Nucleic Acids Res"},{"issue":"7753","key":"pcbi.1008727.ref012","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1038\/s41586-019-0965-1","article-title":"A new genomic blueprint of the human gut microbiota","volume":"568","author":"A Almeida","year":"2019","journal-title":"Nature"},{"key":"pcbi.1008727.ref013","article-title":"A complete domain-to-species taxonomy for Bacteria and Archaea","author":"DH Parks","year":"2020","journal-title":"Nat Biotechnol"},{"key":"pcbi.1008727.ref014","unstructured":"Bai S, Zico Kolter J, Koltun V. 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