title: Computational clustering for viral reference proteomes.
abstract: 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.
  
  
  
  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's 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.
  
  
  
  http://proteininformationresource.org/rps/viruses/
  
  
  
  chenc@udel.edu
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA.
authors.forename: Chuming
authors.initials: C
authors.lastname: Chen
authors.affiliation: Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA.
authors.forename: Hongzhan
authors.initials: H
authors.lastname: Huang
authors.affiliation: Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC 20037, USA.
authors.forename: Raja
authors.initials: R
authors.lastname: Mazumder
authors.affiliation: Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA.
authors.forename: Darren A
authors.initials: DA
authors.lastname: Natale
authors.affiliation: Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA.
authors.forename: Peter B
authors.initials: PB
authors.lastname: McGarvey
authors.affiliation: Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA.
authors.forename: Jian
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA.
authors.forename: Shawn W
authors.initials: SW
authors.lastname: Polson
authors.affiliation: Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA.
authors.forename: Yuqi
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA.
authors.forename: Cathy H
authors.initials: CH
authors.lastname: Wu
mesh_terms: D000595:Amino Acid Sequence; D016000:Cluster Analysis; D019295:Computational Biology; D030562:Databases, Protein; D051188:Knowledge Bases; D020543:Proteome / Q000032:analysis*; D014764:Viral Proteins / Q000032:analysis*
chemical_list: D020543:Proteome; D014764:Viral Proteins