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Viruses 2012, 4(11), 3209-3226; doi:10.3390/v4113209
Article

Virus Pathogen Database and Analysis Resource (ViPR): A Comprehensive Bioinformatics Database and Analysis Resource for the Coronavirus Research Community

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Received: 2 October 2012; in revised form: 13 November 2012 / Accepted: 14 November 2012 / Published: 19 November 2012
(This article belongs to the Special Issue Perspectives and Challenges in Coronavirus Research)
View Full-Text   |   Download PDF [1534 KB, uploaded 19 November 2012]   |   Browse Figures
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 virus; database; bioinformatics; Coronavirus; SARS; SARS-CoV; Coronaviridae; comparative genomics
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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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.

AMA Style

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.

Chicago/Turabian Style

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.


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