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Virus Pathogen Database and Analysis Resource (ViPR): A Comprehensive Bioinformatics Database and Analysis Resource for the Coronavirus Research Community
J. Craig Venter Institute, 10355 Science Center Dr., San Diego, CA 92121, USA
Northrop Grumman Health Solutions, 2101 Gaither Rd., Rockville, MD 20850, USA
Vecna Technologies, 6404 Ivy Lane Suite 500, Greenbelt, MD 20770, USA
* Author to whom correspondence should be addressed.
Received: 2 October 2012; in revised form: 13 November 2012 / Accepted: 14 November 2012 / Published: 19 November 2012
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.
Keywords: virus; database; bioinformatics; Coronavirus; SARS; SARS-CoV; Coronaviridae; comparative genomics
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Cite This Article
MDPI and ACS Style
Pickett, B.E.; Greer, D.S.; Zhang, Y.; Stewart, L.; Zhou, L.; Sun, G.; Gu, Z.; Kumar, S.; Zaremba, S.; Larsen, C.N.; Jen, W.; Klem, E.B.; Scheuermann, R.H. Virus Pathogen Database and Analysis Resource (ViPR): A Comprehensive Bioinformatics Database and Analysis Resource for the Coronavirus Research Community. Viruses 2012, 4, 3209-3226.
Pickett BE, Greer DS, Zhang Y, Stewart L, Zhou L, Sun G, Gu Z, Kumar S, Zaremba S, Larsen CN, Jen W, Klem EB, Scheuermann RH. Virus Pathogen Database and Analysis Resource (ViPR): A Comprehensive Bioinformatics Database and Analysis Resource for the Coronavirus Research Community. Viruses. 2012; 4(11):3209-3226.
Pickett, Brett E.; Greer, Douglas S.; Zhang, Yun; Stewart, Lucy; Zhou, Liwei; Sun, Guangyu; Gu, Zhiping; Kumar, Sanjeev; Zaremba, Sam; Larsen, Christopher N.; Jen, Wei; Klem, Edward B.; Scheuermann, Richard H. 2012. "Virus Pathogen Database and Analysis Resource (ViPR): A Comprehensive Bioinformatics Database and Analysis Resource for the Coronavirus Research Community." Viruses 4, no. 11: 3209-3226.