{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T15:45:34Z","timestamp":1775576734230,"version":"3.50.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2020,3,28]],"date-time":"2020-03-28T00:00:00Z","timestamp":1585353600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["21507012"],"award-info":[{"award-number":["21507012"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["21966015"],"award-info":[{"award-number":["21966015"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002858","name":"China Postdoctoral Science Foundation","doi-asserted-by":"publisher","award":["2015M570329"],"award-info":[{"award-number":["2015M570329"]}],"id":[{"id":"10.13039\/501100002858","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004001","name":"Science and Technology Foundation of Guizhou Province","doi-asserted-by":"publisher","award":["(2019)1287"],"award-info":[{"award-number":["(2019)1287"]}],"id":[{"id":"10.13039\/501100004001","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Joint foundation of GuiZhou Province Science and Technology Commission of China","award":["LH(2017)7176"],"award-info":[{"award-number":["LH(2017)7176"]}]},{"name":"National Science Foundation of Guizhou Provincial Department of Education of China","award":["KY(2015)395"],"award-info":[{"award-number":["KY(2015)395"]}]},{"name":"Startup Foundation for Doctors of Shanxi Medical University","award":["03201503"],"award-info":[{"award-number":["03201503"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Comparing the organization of gene, gene clusters and their flanking genomic contexts is of critical importance to the determination of gene function and evolutionary basis of microbial traits. Currently, user-friendly and flexible tools enabling to visualize and compare genomic contexts for numerous genomes are still missing.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We here present Gcluster, a stand-alone Perl tool that allows researchers to customize and create high-quality linear maps of the genomic region around the genes of interest across large numbers of completed and draft genomes. Importantly, Gcluster integrates homologous gene analysis, in the form of a built-in orthoMCL, and mapping genomes onto a given phylogeny to provide superior comparison of gene contexts.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Gcluster is written in Perl and released under GPLv3. The source code is freely available at https:\/\/github.com\/Xiangyang1984\/Gcluster and http:\/\/www.microbialgenomic.com\/Gcluster_tool.html. Gcluster can also be installed through conda: \u2018conda install -c bioconda gcluster\u2019.<\/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\/btaa212","type":"journal-article","created":{"date-parts":[[2020,3,23]],"date-time":"2020-03-23T12:08:19Z","timestamp":1584965299000},"page":"3871-3873","source":"Crossref","is-referenced-by-count":21,"title":["Gcluster: a simple-to-use tool for visualizing and comparing genome contexts for numerous genomes"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1313-633X","authenticated-orcid":false,"given":"Xiangyang","family":"Li","sequence":"first","affiliation":[{"name":"Department of Environmental Science and Engineering , Fudan University, Shanghai 200433, China"},{"name":"College of Environment and Life Sciences , Kaili University, Kaili 556011, China"}]},{"given":"Fang","family":"Chen","sequence":"additional","affiliation":[{"name":"School of Basic Medical Sciences , Shanxi Medical University, Taiyuan 030001, China"}]},{"given":"Yunpeng","family":"Chen","sequence":"additional","affiliation":[{"name":"Key Laboratory of Urban Agriculture of Ministry of Agriculture School of Agriculture and Biology , Shanghai Jiaotong University, Shanghai 200240, China"}]}],"member":"286","published-online":{"date-parts":[[2020,3,28]]},"reference":[{"key":"2023063011293167500_btaa212-B1","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1186\/1471-2164-9-75","article-title":"The RAST server: rapid annotations using subsystems technology","volume":"9","author":"Aziz","year":"2008","journal-title":"BMC Genomics"},{"key":"2023063011293167500_btaa212-B2","doi-asserted-by":"crossref","first-page":"1394","DOI":"10.1101\/gr.2289704","article-title":"Mauve: multiple alignment of conserved genomic sequence with rearrangements","volume":"14","author":"Darling","year":"2004","journal-title":"Genome Res"},{"key":"2023063011293167500_btaa212-B3","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1093\/bioinformatics\/bty459","article-title":"GeneSpy, a user-friendly and flexible genomic context visualizer","volume":"35","author":"Garcia","year":"2019","journal-title":"Bioinformatics"},{"key":"2023063011293167500_btaa212-B4","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1038\/s41592-018-0046-7","article-title":"Bioconda: sustainable and comprehensive software distribution for the life sciences","volume":"15","author":"Gruning","year":"2018","journal-title":"Nat. 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