{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,27]],"date-time":"2026-01-27T22:45:31Z","timestamp":1769553931723,"version":"3.49.0"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2018,3,29]],"date-time":"2018-03-29T00:00:00Z","timestamp":1522281600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100011512","name":"National Research Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100011512","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007431","name":"NRF","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007431","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Ministry of Science","award":["ICT &"],"award-info":[{"award-number":["ICT &"]}]},{"name":"Future Planning, Basic Science Research Program"},{"DOI":"10.13039\/501100003621","name":"MSIP","doi-asserted-by":"publisher","award":["NRF-2016R1C1B1007929"],"award-info":[{"award-number":["NRF-2016R1C1B1007929"]}],"id":[{"id":"10.13039\/501100003621","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009950","name":"Ministry of Education","doi-asserted-by":"publisher","award":["2015R1D1A1A01057899"],"award-info":[{"award-number":["2015R1D1A1A01057899"]}],"id":[{"id":"10.13039\/100009950","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009950","name":"Ministry of Education","doi-asserted-by":"publisher","award":["2016R1D1A1A09919318"],"award-info":[{"award-number":["2016R1D1A1A09919318"]}],"id":[{"id":"10.13039\/100009950","id-type":"DOI","asserted-by":"publisher"}]},{"name":"2017 Hongik University Research Fund"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Next-generation sequencing (NGS) technologies have led to the accumulation of high-throughput sequence data from various organisms in biology. To apply gene annotation of organellar genomes for various organisms, more optimized tools for functional gene annotation are required. Almost all gene annotation tools are mainly focused on the chloroplast genome of land plants or the mitochondrial genome of animals. We have developed a web application AGORA for the fast, user-friendly and improved annotations of organellar genomes. Annotator for Genes of Organelle from the Reference sequence Analysis (AGORA) annotates genes based on a basic local alignment search tool (BLAST)-based homology search and clustering with selected reference sequences from the NCBI database or user-defined uploaded data. AGORA can annotate the functional genes in almost all mitochondrion and plastid genomes of eukaryotes. The gene annotation of a genome with an exon\u2013intron structure within a gene or inverted repeat region is also available. It provides information of start and end positions of each gene, BLAST results compared with the reference sequence and visualization of gene map by OGDRAW.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Users can freely use the software, and the accessible URL is https:\/\/bigdata.dongguk.edu\/gene_project\/AGORA\/. The main module of the tool is implemented by the python and php, and the web page is built by the HTML and CSS to support all browsers.<\/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\/bty196","type":"journal-article","created":{"date-parts":[[2018,3,28]],"date-time":"2018-03-28T11:32:05Z","timestamp":1522236725000},"page":"2661-2663","source":"Crossref","is-referenced-by-count":45,"title":["AGORA: organellar genome annotation from the amino acid and nucleotide references"],"prefix":"10.1093","volume":"34","author":[{"given":"Jaehee","family":"Jung","sequence":"first","affiliation":[{"name":"Department of General Education, Hongik University, Seoul, Korea"}]},{"given":"Jong Im","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Biology, Chungnam National University, Daejeon, Korea"}]},{"given":"Young-Sik","family":"Jeong","sequence":"additional","affiliation":[{"name":"Department of Multimedia Engineering, Dongguk University, Seoul, Korea"}]},{"given":"Gangman","family":"Yi","sequence":"additional","affiliation":[{"name":"Department of Multimedia Engineering, Dongguk University, Seoul, Korea"}]}],"member":"286","published-online":{"date-parts":[[2018,3,29]]},"reference":[{"key":"2023012713082870100_bty196-B1","doi-asserted-by":"crossref","first-page":"1436","DOI":"10.1093\/molbev\/msq029","article-title":"Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae)","volume":"27","author":"Alverson","year":"2010","journal-title":"Mol. Biol. Evol."},{"key":"2023012713082870100_bty196-B2","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1186\/1471-2164-13-715","article-title":"CpGAVAS, an integrated web server for the annotation, visualization, analysis, and genbank submission of completely sequenced chloroplast genome sequences","volume":"13","author":"Liu","year":"2012","journal-title":"BMC Genomics"},{"key":"2023012713082870100_bty196-B3","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1007\/s00294-007-0161-y","article-title":"OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes","volume":"52","author":"Lohse","year":"2007","journal-title":"Curr. Genet"},{"key":"2023012713082870100_bty196-B4","doi-asserted-by":"crossref","first-page":"W575","DOI":"10.1093\/nar\/gkt289","article-title":"OrganellarGenomeDRAW\u2014a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets","volume":"41","author":"Lohse","year":"2013","journal-title":"Nucl. Acids Res"},{"key":"2023012713082870100_bty196-B5","first-page":"130","article-title":"Verdant: automated annotation, alignment and phylogenetic analysis of whole chloroplast genomes","volume-title":"Bioinformatics","author":"McKain","year":"2017"},{"key":"2023012713082870100_bty196-B6","volume-title":"Bootstrap: Responsive Web Development","author":"Spurlock","year":"2013"},{"key":"2023012713082870100_bty196-B7","doi-asserted-by":"crossref","first-page":"W6","DOI":"10.1093\/nar\/gkx391","article-title":"GeSeq\u2014versatile and accurate annotation of organelle genomes","volume":"45","author":"Tillich","year":"2017","journal-title":"Nucl. Acids Res"},{"key":"2023012713082870100_bty196-B8","doi-asserted-by":"crossref","first-page":"3252.","DOI":"10.1093\/bioinformatics\/bth352","article-title":"Automatic annotation of organellar genomes with DOGMA","volume":"20","author":"Wyman","year":"2004","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/15\/2661\/48935386\/bioinformatics_34_15_2661.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/15\/2661\/48935386\/bioinformatics_34_15_2661.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T14:13:35Z","timestamp":1674828815000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/15\/2661\/4956347"}},"subtitle":[],"editor":[{"given":"Inanc","family":"Birol","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,3,29]]},"references-count":8,"journal-issue":{"issue":"15","published-print":{"date-parts":[[2018,8,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty196","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,8,1]]},"published":{"date-parts":[[2018,3,29]]}}}