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

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.

Figure 1.

Online Bioinformatics Tools Provided in ViPR. Various bioinformatics analyses can be performed, visualized and stored on the ViPR server. (A) A phylogenetic tree, in Archaeopteryx, colored by country of isolation with dark gray, light brown, tan, orange, red, dark red, blue and light gray representing viruses isolated in Vietnam, United States, Cambodia, Venezuela, Colombia, Nicaragua, Ecuador and Brazil, respectively. Strains belonging to the four serotypes are indicated. The blue text and brace indicate DENV-2 strains belonging to a Nicaraguan lineage, whereas the orange text and brace delineate DENV-2 strains from a Brazilian lineage. (B) A portion of a multiple sequence alignment, visualized with JalView, constructed using MUSCLE from the nucleotide sequences for the DENV use case. (C) The Sequence Feature Details page showing the SF metadata and the VTs for a β-strand structure in the DENV-2 E protein, named Dengue_Virus_2_Beta-straind_617(8), spanning positions 617–624 of the polyprotein. (D) A DENV E protein structure (PDB: 1OK8) in the ViPR implementation of the Jmol structure viewer with α-helices in magenta, β-strands in yellow and the SF from (C) highlighted in cyan.