Virus Pathogen Resource (ViPR)

Virus Pathogen Resource (ViPR) provides integrated viral sequence, annotation, three-dimensional structure, immune epitope, and metadata resources with analytical tools for comparative genomics, phylogenetics, and sequence-variation analyses of human pathogenic and emerging viruses.

Key Features:

• Comprehensive data holdings: Sequence records, gene and protein annotations, three-dimensional protein structures, immune epitope locations, clinical and surveillance metadata, and host factor information.
• Virus family coverage: Data and analyses for Arenaviridae, Bunyaviridae, Caliciviridae, Coronaviridae, Flaviviridae, Filoviridae, Hepeviridae, Herpesviridae, Paramyxoviridae, Picornaviridae, Poxviridae, Reoviridae, Rhabdoviridae, and Togaviridae.
• Analytical toolset: Metadata-driven statistical sequence analysis, multiple sequence alignment, phylogenetic tree construction, BLAST comparison, sequence variation determination, and comparative genomics analysis.
• Structural and epitope analysis: Integration of three-dimensional protein structures, 3D structure visualization, and immune epitope mapping.
• Reference annotation transfer: Transfer of existing reference genome annotations to new genomes.
• Data integration: Integrated analyses combining sequence, annotation, structure, epitope, and clinical/surveillance metadata.
• Support and affiliation: Supported by the National Institute of Allergy and Infectious Diseases (NIAID) Bioinformatics Resource Centers (BRC) program.

Scientific Applications:

• Comparative genomics: Identification of conserved and variable genomic regions using metadata-driven comparative analyses.
• Phylogenetics and molecular epidemiology: Phylogenetic inference and tree construction for evolutionary and epidemiological studies.
• Variant and sequence-variation analysis: Detection and mapping of sequence variation to annotations and structures.
• Epitope and immune response research: Mapping immune epitopes and analyzing antigenic regions for vaccine and immune-studies.
• Structural interpretation: Contextualizing sequence variation and epitopes on three-dimensional protein structures.
• Countermeasure development support: Integrated sequence, epitope, and structural analyses to support development of diagnostics, prophylactics, vaccines, and therapeutics.
• Coronaviridae research: Targeted analyses for Coronaviridae, including Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), using sequence, epitope, and structural datasets.

Methodology:

Methods explicitly include metadata-driven statistical sequence analysis, multiple sequence alignment, phylogenetic tree construction, BLAST comparison, sequence variation determination, comparative genomics analysis, three-dimensional protein structure visualization, and transfer of reference genome annotations to new genomes.