{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,16]],"date-time":"2026-04-16T16:37:02Z","timestamp":1776357422281,"version":"3.51.2"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2017,12,8]],"date-time":"2017-12-08T00:00:00Z","timestamp":1512691200000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 GM70641"],"award-info":[{"award-number":["R01 GM70641"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Summary<\/jats:title><jats:p>The examination of gene neighborhood is an integral part of comparative genomics but no tools to produce publication quality graphics of gene clusters are available. Gene Graphics is a straightforward web application for creating such visuals. Supported inputs include National Center for Biotechnology Information gene and protein identifiers with automatic fetching of neighboring information, GenBank files and data extracted from the SEED database. Gene representations can be customized for many parameters including gene and genome names, colors and sizes. Gene attributes can be copied and pasted for rapid and user-friendly customization of homologous genes between species. In addition to Portable Network Graphics and Scalable Vector Graphics, produced representations can be exported as Tagged Image File Format or Encapsulated PostScript, formats that are standard for publication. Hands-on tutorials with real life examples inspired from publications are available for training.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>Gene Graphics is freely available at https:\/\/katlabs.cc\/genegraphics\/ and source code is hosted at https:\/\/github.com\/katlabs\/genegraphics.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx793","type":"journal-article","created":{"date-parts":[[2017,12,5]],"date-time":"2017-12-05T20:16:47Z","timestamp":1512505007000},"page":"1406-1408","source":"Crossref","is-referenced-by-count":116,"title":["Gene Graphics: a genomic neighborhood data visualization web application"],"prefix":"10.1093","volume":"34","author":[{"given":"Katherine J","family":"Harrison","sequence":"first","affiliation":[{"name":"Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA"}]},{"given":"Val\u00e9rie de","family":"Cr\u00e9cy-Lagard","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA"}]},{"given":"R\u00e9mi","family":"Zallot","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA"}]}],"member":"286","published-online":{"date-parts":[[2017,12,7]]},"reference":[{"key":"2023012713011422700_btx793-B1","doi-asserted-by":"crossref","first-page":"D34","DOI":"10.1093\/nar\/gki063","article-title":"GenBank","volume":"33","author":"Benson","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"2023012713011422700_btx793-B2","doi-asserted-by":"crossref","first-page":"2334","DOI":"10.1093\/bioinformatics\/btq413","article-title":"genoPlotR: comparative gene and genome visualization in R","volume":"26","author":"Guy","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012713011422700_btx793-B3","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1038\/nchembio.2108","article-title":"A family of metal-dependent phosphatases implicated in metabolite damage-control","volume":"12","author":"Huang","year":"2016","journal-title":"Nat. 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