ViPR: an open bioinformatics database and analysis resource for virology research

• Published in: Nucleic acids research Vol. 40; no. D1; pp. D593 - D598
• Main Authors: Pickett, Brett E., Sadat, Eva L., Zhang, Yun, Noronha, Jyothi M., Squires, R. Burke, Hunt, Victoria, Liu, Mengya, Kumar, Sanjeev, Zaremba, Sam, Gu, Zhiping, Zhou, Liwei, Larson, Christopher N., Dietrich, Jonathan, Klem, Edward B., Scheuermann, Richard H.
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.01.2012
• Subjects: Arenaviridae; Bioinformatics; Computational Biology; Databases, Genetic; Genes, Viral; Phylogeny; Sequence Alignment; Sequence Analysis; Software; Viral Proteins - chemistry; Viruses - classification; Viruses - genetics
• ISSN: 0305-1048; 1362-4962; 1362-4954; 1362-4962
• DOI: 10.1093/nar/gkr859

The Virus Pathogen Database and Analysis Resource (ViPR, www.ViPRbrc.org) is an integrated repository of data and analysis tools for multiple virus families, supported by the National Institute of Allergy and Infectious Diseases (NIAID) Bioinformatics Resource Centers (BRC) program. ViPR contains information for human pathogenic viruses belonging to the Arenaviridae, Bunyaviridae, Caliciviridae, Coronaviridae, Flaviviridae, Filoviridae, Hepeviridae, Herpesviridae, Paramyxoviridae, Picornaviridae, Poxviridae, Reoviridae, Rhabdoviridae and Togaviridae families, with plans to support additional virus families in the future. ViPR captures various types of information, including sequence records, gene and protein annotations, 3D protein structures, immune epitope locations, clinical and surveillance metadata and novel data derived from comparative genomics analysis. Analytical and visualization tools for metadata-driven statistical sequence analysis, multiple sequence alignment, phylogenetic tree construction, BLAST comparison and sequence variation determination are also provided. Data filtering and analysis workflows can be combined and the results saved in personal 'Workbenches' for future use. ViPR tools and data are available without charge as a service to the virology research community to help facilitate the development of diagnostics, prophylactics and therapeutics for priority pathogens and other viruses.