title: Virus pathogen database and analysis resource (ViPR): a comprehensive bioinformatics database and analysis resource for the coronavirus research community.
abstract: Several viruses within the Coronaviridae family have been categorized as either emerging or re-emerging human pathogens, with Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) being the most well known. The NIAID-sponsored Virus Pathogen Database and Analysis Resource (ViPR, www.viprbrc.org) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses, including the entire Coronaviridae family. ViPR provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, host factor data, and other data types through an intuitive web-based search interface. Records returned from these queries can then be subjected to web-based analyses including: multiple sequence alignment, phylogenetic inference, sequence variation determination, BLAST comparison, and metadata-driven comparative genomics statistical analysis. Additional tools exist to display multiple sequence alignments, view phylogenetic trees, visualize 3D protein structures, transfer existing reference genome annotations to new genomes, and store or share results from any search or analysis within personal private 'Workbench' spaces for future access. All of the data and integrated analysis and visualization tools in ViPR are made available without charge as a service to the Coronaviridae research community to facilitate the research and development of diagnostics, prophylactics, vaccines and therapeutics against these human pathogens.
authors.affiliation: J. Craig Venter Institute, 10355 Science Center Dr., San Diego, CA 92121, USA. bpickett@jcvi.org
authors.forename: Brett E
authors.initials: BE
authors.lastname: Pickett
authors.forename: Douglas S
authors.initials: DS
authors.lastname: Greer
authors.forename: Yun
authors.initials: Y
authors.lastname: Zhang
authors.forename: Lucy
authors.initials: L
authors.lastname: Stewart
authors.forename: Liwei
authors.initials: L
authors.lastname: Zhou
authors.forename: Guangyu
authors.initials: G
authors.lastname: Sun
authors.forename: Zhiping
authors.initials: Z
authors.lastname: Gu
authors.forename: Sanjeev
authors.initials: S
authors.lastname: Kumar
authors.forename: Sam
authors.initials: S
authors.lastname: Zaremba
authors.forename: Christopher N
authors.initials: CN
authors.lastname: Larsen
authors.forename: Wei
authors.initials: W
authors.lastname: Jen
authors.forename: Edward B
authors.initials: EB
authors.lastname: Klem
authors.forename: Richard H
authors.initials: RH
authors.lastname: Scheuermann
mesh_terms: D019295:Computational Biology / Q000379:methods; D017934:Coronavirus; D016208:Databases, Factual; D006801:Humans; D020407:Internet; D054579:National Institute of Allergy and Infectious Diseases (U.S.); D012106:Research; D057386:Search Engine; D012984:Software; D014481:United States; D014584:User-Computer Interface