{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,6]],"date-time":"2025-11-06T20:02:31Z","timestamp":1762459351689},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"13","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The enormous number of redundant sequenced genomes has hindered efforts to analyze and functionally annotate proteins. As the taxonomy of viruses is not uniformly defined, viral proteomes pose special challenges in this regard. Grouping viruses based on the similarity of their proteins at proteome scale can normalize against potential taxonomic nomenclature anomalies.<\/jats:p>\n               <jats:p>Results: We present Viral Reference Proteomes (Viral RPs), which are computed from complete virus proteomes within UniProtKB. Viral RPs based on 95, 75, 55, 35 and 15% co-membership in proteome similarity based clusters are provided. Comparison of our computational Viral RPs with UniProt\u2019s curator-selected Reference Proteomes indicates that the two sets are consistent and complementary. Furthermore, each Viral RP represents a cluster of virus proteomes that was consistent with virus or host taxonomy. We provide BLASTP search and FTP download of Viral RP protein sequences, and a browser to facilitate the visualization of Viral RPs.<\/jats:p>\n               <jats:p>Availability and implementation: \u00a0http:\/\/proteininformationresource.org\/rps\/viruses\/<\/jats:p>\n               <jats:p>Contact: \u00a0chenc@udel.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw110","type":"journal-article","created":{"date-parts":[[2016,2,27]],"date-time":"2016-02-27T02:10:41Z","timestamp":1456539041000},"page":"2041-2043","source":"Crossref","is-referenced-by-count":3,"title":["Computational clustering for viral reference proteomes"],"prefix":"10.1093","volume":"32","author":[{"given":"Chuming","family":"Chen","sequence":"first","affiliation":[{"name":"1 Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hongzhan","family":"Huang","sequence":"additional","affiliation":[{"name":"1 Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Raja","family":"Mazumder","sequence":"additional","affiliation":[{"name":"2 Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC 20037, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Darren A.","family":"Natale","sequence":"additional","affiliation":[{"name":"3 Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter B.","family":"McGarvey","sequence":"additional","affiliation":[{"name":"3 Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jian","family":"Zhang","sequence":"additional","affiliation":[{"name":"3 Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shawn W.","family":"Polson","sequence":"additional","affiliation":[{"name":"1 Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuqi","family":"Wang","sequence":"additional","affiliation":[{"name":"1 Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cathy H.","family":"Wu","sequence":"additional","affiliation":[{"name":"1 Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA"},{"name":"3 Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"name":"UniProt Consortium","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,2,26]]},"reference":[{"key":"2023020112333087600_btw110-B1","doi-asserted-by":"crossref","first-page":"e18910.","DOI":"10.1371\/journal.pone.0018910","article-title":"Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation","volume":"6","author":"Chen","year":"2011","journal-title":"PLoS ONE"},{"key":"2023020112333087600_btw110-B2","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1016\/j.virol.2014.08.024","article-title":"Understanding the enormous diversity of bacteriophages: the tailed phages that infect the bacterial family Enterobacteriaceae","volume":"468\u2013470","author":"Grose","year":"2014","journal-title":"Virology"},{"key":"2023020112333087600_btw110-B3","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1016\/j.virol.2007.03.047","article-title":"Analysis of the phage sequence space: the benefit of structured information","volume":"365","author":"Lima-Mendez","year":"2007","journal-title":"Virology"},{"key":"2023020112333087600_btw110-B4","doi-asserted-by":"crossref","first-page":"D6","DOI":"10.1093\/nar\/gku1130","article-title":"Database resources of the National Center for Biotechnology Information","volume":"43","author":"NCBI Resource Coordinators","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023020112333087600_btw110-B5","doi-asserted-by":"crossref","first-page":"4529","DOI":"10.1128\/JB.184.16.4529-4535.2002","article-title":"The phage proteomic tree: a genome-based taxonomy for phage","volume":"184","author":"Rohwer","year":"2002","journal-title":"J. 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