{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,28]],"date-time":"2026-06-28T13:36:49Z","timestamp":1782653809494,"version":"3.54.5"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2019,5,4]],"date-time":"2019-05-04T00:00:00Z","timestamp":1556928000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31871330"],"award-info":[{"award-number":["31871330"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>OrthoVenn is a powerful web platform for the comparison and analysis of whole-genome orthologous clusters. Here we present an updated version, OrthoVenn2, which provides new features that facilitate the comparative analysis of orthologous clusters among up to 12 species. Additionally, this update offers improvements to data visualization and interpretation, including an occurrence pattern table for interrogating the overlap of each orthologous group for the queried species. Within the occurrence table, the functional annotations and summaries of the disjunctions and intersections of clusters between the chosen species can be displayed through an interactive Venn diagram. To facilitate a broader range of comparisons, a larger number of species, including vertebrates, metazoa, protists, fungi, plants and bacteria, have been added in OrthoVenn2. Finally, a stand-alone version is available to perform large dataset comparisons and to visualize results locally without limitation of species number. In summary, OrthoVenn2 is an efficient and user-friendly web server freely accessible at https:\/\/orthovenn2.bioinfotoolkits.net.<\/jats:p>","DOI":"10.1093\/nar\/gkz333","type":"journal-article","created":{"date-parts":[[2019,4,25]],"date-time":"2019-04-25T11:23:00Z","timestamp":1556191380000},"page":"W52-W58","source":"Crossref","is-referenced-by-count":757,"title":["OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species"],"prefix":"10.1093","volume":"47","author":[{"given":"Ling","family":"Xu","sequence":"first","affiliation":[{"name":"Biological Science Research Center, Southwest University, Chongqing 400715, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1275-581X","authenticated-orcid":false,"given":"Zhaobin","family":"Dong","sequence":"additional","affiliation":[{"name":"Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA\u00a094710,\u00a0USA"},{"name":"USDA-ARS, Plant Gene Expression Center, Albany, CA 94706, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lu","family":"Fang","sequence":"additional","affiliation":[{"name":"Biological Science Research Center, Southwest University, Chongqing 400715, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongjiang","family":"Luo","sequence":"additional","affiliation":[{"name":"Biological Science Research Center, Southwest University, Chongqing 400715, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhaoyuan","family":"Wei","sequence":"additional","affiliation":[{"name":"Biological Science Research Center, Southwest University, Chongqing 400715, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hailong","family":"Guo","sequence":"additional","affiliation":[{"name":"Biological Science Research Center, Southwest University, Chongqing 400715, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guoqing","family":"Zhang","sequence":"additional","affiliation":[{"name":"Biological Science Research Center, Southwest University, Chongqing 400715, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yong Q","family":"Gu","sequence":"additional","affiliation":[{"name":"USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94706, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Devin","family":"Coleman-Derr","sequence":"additional","affiliation":[{"name":"Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA\u00a094710,\u00a0USA"},{"name":"USDA-ARS, Plant Gene Expression Center, Albany, CA 94706, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qingyou","family":"Xia","sequence":"additional","affiliation":[{"name":"Biological Science Research Center, Southwest University, Chongqing 400715, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi","family":"Wang","sequence":"additional","affiliation":[{"name":"Biological Science Research Center, Southwest University, Chongqing 400715, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,5,4]]},"reference":[{"key":"2019062808131656400_B1","doi-asserted-by":"crossref","first-page":"interactions1002.1","DOI":"10.1186\/gb-2001-2-8-interactions1002","article-title":"Orthologs and paralogs - we need to get it right","volume":"2","author":"Jensen","year":"2001","journal-title":"Genome Biol."},{"key":"2019062808131656400_B2","doi-asserted-by":"crossref","first-page":"e1000703","DOI":"10.1371\/journal.pcbi.1000703","article-title":"Getting started in gene orthology and functional analysis","volume":"6","author":"Fang","year":"2010","journal-title":"PLoS Comput. 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