The Virus Pathogen Database and Analysis Resource (ViPR) is an integrative and comprehensive publicly available database and analysis resource to search, analyze, visualize, save and share data for viral pathogens in the U.S. National Institute of Allergy and Infectious Diseases (NIAID) Category A-C Priority Pathogen lists for biodefense research, and other viral pathogens causing emerging/reemerging infectious diseases. ViPR is one of the five Bioinformatics Resource Centers (BRC) funded by NIAID, a component of the National Institutes of Health (NIH), which is an agency of the United States Department of Health and Human Services.
The ViPR database includes genomes from these viral families: Arenaviridae, Bunyaviridae, Caliciviridae, Coronaviridae, Filoviridae, Flaviviridae, Hepeviridae, Herpesviridae, Paramyxoviridae, Picornaviridae, Poxviridae, Reoviridae, Rhabdoviridae, and Togaviridae.
GenomesGenome annotationsGenes & proteinsPredicted protein domains and motifsImmune epitopesSequence Features Orthologous protein clusters3D protein structureClinical metadataHost factor dataBLAST: provides a variety of custom ViPR databases to identify the most related sequence(s)Short Peptide Search: allows users to find any peptide sequence using exact, fuzzy, or pattern matchingSequence Variation Analysis ([Single-nucleotide polymorphism] SNP): calculates sequence variation existing in the specified sequencesMetadata-driven Comparative Analysis Tool for Sequences (Meta-CATS): an automated comparative statistical analysis to identify positions throughout a multiple sequence alignment that significantly differ between groups of sequences possessing specific phenotypic characteristicMultiple Sequence Alignment: aligns small genomes, gene/protein sequences or large viral genome sequences using one of several algorithm best-suited for the specific job submissionSequence Alignment Visualization: uses JalView for sequence alignment visualizationPhylogenetic Tree Generation: calculates a tree using one of several available algorithms and evolutionary modelsPhylogenetic Tree Visualization: allows the color-coded display of strain metadata on a tree using the Archaeopteryx viewerGBrowse: provides genome browsing capability for large DNA viral genomes (Herpesviridae and Poxviridae) with integration of ViPR Sequence Features for Vaccinia virusSequence Feature Variant Type (SFVT) analysis: provides a centralized repository of functional regions and automatically calculates all observed sequence variation within each defined region3D Protein Structure Visualization: integrates PDB protein structure files with ViPR Sequence Features when applicable and provides an interactive 3D protein structure viewer using JmolGenome Annotator (GATU): allows users to annotate new genome sequences provided by the userGenotype Determination and Recombination Detection: predicts the genotype for user-provided sequences and identifies possible sites of recombination for viruses in the Flaviviridae familyPCR Primer Design: allows the user to automatically predict ideal primers based on a sequence and specified parametersReadSeq: converts between various sequence formatsSequence Feature Submission Tool: allows users to define a Sequence Feature by filling out a webformExternal Analysis Tools: displays a list and description of third-party tools for more specialized analysesPersonal Workbench to save and share data and analysis