ViPR: an open bioinformatics database and analysis resource for virology research
Open Access
- 17 October 2011
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 40 (D1), D593-D598
- https://doi.org/10.1093/nar/gkr859
Abstract
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.Keywords
This publication has 34 references indexed in Scilit:
- Database resources of the National Center for Biotechnology InformationNucleic Acids Research, 2010
- Ongoing and future developments at the Universal Protein ResourceNucleic Acids Research, 2010
- Evidence for separation of HCV subtype 1a into two distinct cladesJournal of Viral Hepatitis, 2010
- The Immune Epitope Database 2.0Nucleic Acids Research, 2009
- Jalview Version 2—a multiple sequence alignment editor and analysis workbenchBioinformatics, 2009
- BioHealthBase: informatics support in the elucidation of influenza virus host–pathogen interactions and virulenceNucleic Acids Research, 2007
- WebLogo: A Sequence Logo Generator: Figure 1Genome Research, 2004
- MUSCLE: multiple sequence alignment with high accuracy and high throughputNucleic Acids Research, 2004
- OrthoMCL: Identification of Ortholog Groups for Eukaryotic GenomesGenome Research, 2003
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997