{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T04:43:18Z","timestamp":1774932198730,"version":"3.50.1"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2022,5,26]],"date-time":"2022-05-26T00:00:00Z","timestamp":1653523200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Programme for Fostering Excellence in Scientific and Technical Research","award":["PGC2018-098073-A-I00"],"award-info":[{"award-number":["PGC2018-098073-A-I00"]}]},{"DOI":"10.13039\/100010434","name":"\u2018la Caixa\u2019 Foundation","doi-asserted-by":"publisher","award":["100010434"],"award-info":[{"award-number":["100010434"]}],"id":[{"id":"10.13039\/100010434","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European Union's Horizon 2020"},{"name":"Marie Sk\u0142odowska-Curie","award":["713673"],"award-info":[{"award-number":["713673"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Synteny conservation analysis is a well-established methodology to investigate the potential functional role of unknown prokaryotic genes. However, bioinformatic tools to reconstruct and visualise genomic contexts usually depend on slow computations, are restricted to narrow taxonomic ranges, and\/or do not allow for the functional and interactive exploration of neighbouring genes across different species. Here, we present GeCoViz, an online resource built upon 12 221 reference prokaryotic genomes that provides fast and interactive visualisation of custom genomic regions anchored by any target gene, which can be sought by either name, orthologous group (KEGGs, eggNOGs), protein domain (PFAM) or sequence. To facilitate functional and evolutionary interpretation, GeCoViz allows to customise the taxonomic scope of each analysis and provides comprehensive annotations of the neighbouring genes. Interactive visualisation options include, among others, the scaled representations of gene lengths and genomic distances, and on the fly calculation of synteny conservation of neighbouring genes, which can be highlighted based on custom thresholds. The resulting plots can be downloaded as high-quality images for publishing purposes. Overall, GeCoViz offers an easy-to-use, comprehensive, fast and interactive web-based tool for investigating the genomic context of prokaryotic genes, and is freely available at https:\/\/gecoviz.cgmlab.org<\/jats:p>","DOI":"10.1093\/nar\/gkac367","type":"journal-article","created":{"date-parts":[[2022,5,5]],"date-time":"2022-05-05T20:09:12Z","timestamp":1651781352000},"page":"W352-W357","source":"Crossref","is-referenced-by-count":28,"title":["GeCoViz: genomic context visualisation of prokaryotic genes from a functional and evolutionary perspective"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7292-8981","authenticated-orcid":false,"given":"Jorge","family":"Botas","sequence":"first","affiliation":[{"name":"Centro de Biotecnolog\u00eda y Gen\u00f3mica de Plantas, Universidad Polit\u00e9cnica de Madrid (UPM) - Instituto Nacional de Investigaci\u00f3n y Tecnolog\u00eda Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo-UPM , Madrid , 28223, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3907-3904","authenticated-orcid":false,"given":"\u00c1lvaro","family":"Rodr\u00edguez\u00a0del\u00a0R\u00edo","sequence":"additional","affiliation":[{"name":"Centro de Biotecnolog\u00eda y Gen\u00f3mica de Plantas, Universidad Polit\u00e9cnica de Madrid (UPM) - Instituto Nacional de Investigaci\u00f3n y Tecnolog\u00eda Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo-UPM , Madrid , 28223, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1553-8295","authenticated-orcid":false,"given":"Joaqu\u00edn","family":"Giner-Lamia","sequence":"additional","affiliation":[{"name":"Centro de Biotecnolog\u00eda y Gen\u00f3mica de Plantas, Universidad Polit\u00e9cnica de Madrid (UPM) - Instituto Nacional de Investigaci\u00f3n y Tecnolog\u00eda Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo-UPM , Madrid , 28223, Spain"},{"name":"Departamento de Biotecnolog\u00eda-Biolog\u00eda Vegetal, Escuela T\u00e9cnica Superior de Ingenier\u00eda Agron\u00f3mica, Alimentaria y de Biosistemas, Universidad Polit\u00e9cnica de Madrid (UPM) , Madrid , 28040,\u00a0 Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4195-5025","authenticated-orcid":false,"given":"Jaime","family":"Huerta-Cepas","sequence":"additional","affiliation":[{"name":"Centro de Biotecnolog\u00eda y Gen\u00f3mica de Plantas, Universidad Polit\u00e9cnica de Madrid (UPM) - Instituto Nacional de Investigaci\u00f3n y Tecnolog\u00eda Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo-UPM , Madrid , 28223, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,5,26]]},"reference":[{"key":"2022070500014913700_B1","doi-asserted-by":"crossref","first-page":"11399","DOI":"10.1073\/pnas.1614083113","article-title":"Theory of prokaryotic genome evolution","volume":"113","author":"Sela","year":"2016","journal-title":"Proc. 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