{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T00:03:48Z","timestamp":1775865828115,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2017,11,2]],"date-time":"2017-11-02T00:00:00Z","timestamp":1509580800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001691","name":"JSPS","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome submission to public sequence databases. DFAST was originally started as an on-line annotation server, and to date, over 7000 jobs have been processed since its first launch in 2016. Here, we present a newly implemented background annotation engine for DFAST, which is also available as a standalone command-line program. The new engine can annotate a typical-sized bacterial genome within 10\u2009min, with rich information such as pseudogenes, translation exceptions and orthologous gene assignment between given reference genomes. In addition, the modular framework of DFAST allows users to customize the annotation workflow easily and will also facilitate extensions for new functions and incorporation of new tools in the future.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The software is implemented in Python 3 and runs in both Python 2.7 and 3.4\u2014on Macintosh and Linux systems. It is freely available at https:\/\/github.com\/nigyta\/dfast_core\/under the GPLv3 license with external binaries bundled in the software distribution. An on-line version is also available at https:\/\/dfast.nig.ac.jp\/.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx713","type":"journal-article","created":{"date-parts":[[2017,11,1]],"date-time":"2017-11-01T12:10:24Z","timestamp":1509538224000},"page":"1037-1039","source":"Crossref","is-referenced-by-count":1150,"title":["DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication"],"prefix":"10.1093","volume":"34","author":[{"given":"Yasuhiro","family":"Tanizawa","sequence":"first","affiliation":[{"name":"Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Japan"}]},{"given":"Takatomo","family":"Fujisawa","sequence":"additional","affiliation":[{"name":"Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Japan"}]},{"given":"Yasukazu","family":"Nakamura","sequence":"additional","affiliation":[{"name":"Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Japan"}]}],"member":"286","published-online":{"date-parts":[[2017,11,2]]},"reference":[{"key":"2023012712470040500_btx713-B1","doi-asserted-by":"crossref","first-page":"D48","DOI":"10.1093\/nar\/gkv1323","article-title":"The International Nucleotide Sequence Database Collaboration","volume":"44","author":"Cochrane","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023012712470040500_btx713-B2","doi-asserted-by":"crossref","first-page":"D387","DOI":"10.1093\/nar\/gks1234","article-title":"TIGRFAMs and genome properties in 2013","volume":"41","author":"Haft","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023012712470040500_btx713-B3","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1101\/gr.113985.110","article-title":"Adaptive seeds tame genomic sequence comparison","volume":"21","author":"Kie\u0142basa","year":"2011","journal-title":"Genome Res"},{"key":"2023012712470040500_btx713-B4","doi-asserted-by":"crossref","first-page":"D200","DOI":"10.1093\/nar\/gkw1129","article-title":"CDD\/SPARCLE: functional classification of proteins via subfamily domain architectures","volume":"45","author":"Marchler-Bauer","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023012712470040500_btx713-B5","doi-asserted-by":"crossref","first-page":"D25","DOI":"10.1093\/nar\/gkw1001","article-title":"DNA Data Bank of Japan","volume":"45","author":"Mashima","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023012712470040500_btx713-B6","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"2023012712470040500_btx713-B7","author":"Sugawara","year":"2009"},{"key":"2023012712470040500_btx713-B8","doi-asserted-by":"crossref","first-page":"e103833","DOI":"10.1371\/journal.pone.0103833","article-title":"GHOSTX: an improved sequence homology search algorithm using a query suffix array and a database suffix array","volume":"9","author":"Suzuki","year":"2014","journal-title":"PLoS ONE"},{"key":"2023012712470040500_btx713-B9","first-page":"173","article-title":"DFAST and DAGA: Web-based integrated genome annotation tools and resources","volume":"35","author":"Tanizawa","year":"2016","journal-title":"BMFH"},{"key":"2023012712470040500_btx713-B10","doi-asserted-by":"crossref","first-page":"6614","DOI":"10.1093\/nar\/gkw569","article-title":"NCBI prokaryotic genome annotation pipeline","volume":"44","author":"Tatusova","year":"2016","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/6\/1037\/48913703\/bioinformatics_34_6_1037.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/6\/1037\/48913703\/bioinformatics_34_6_1037.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T13:39:21Z","timestamp":1674826761000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/6\/1037\/4587587"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,11,2]]},"references-count":10,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2018,3,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx713","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,3,15]]},"published":{"date-parts":[[2017,11,2]]}}}