Virus Pathogen Database and Analysis Resource

Virus families covered in ViPR

Data types in ViPR

• Genomes
• Genome annotations
• Genes & proteins
• Predicted protein domains and motifs
• Immune epitopes
• Sequence Features
• Orthologous protein clusters
• 3D protein structure
• Clinical metadata
• Host factor data

  Analysis and visualization tools in ViPR

• BLAST: provides a variety of custom ViPR databases to identify the most related sequence
• Short Peptide Search: allows users to find any peptide sequence using exact, fuzzy, or pattern matching
• Sequence Variation Analysis : calculates sequence variation existing in the specified sequences
• Metadata-driven Comparative Analysis Tool for Sequences : an automated comparative statistical analysis to identify positions throughout a multiple sequence alignment that significantly differ between groups of sequences possessing specific phenotypic characteristic
• Multiple Sequence Alignment: aligns small genomes, gene/protein sequences or large viral genome sequences using one of several algorithm best-suited for the specific job submission
• Sequence Alignment Visualization: uses JalView for sequence alignment visualization
• Phylogenetic Tree Generation: calculates a tree using one of several available algorithms and evolutionary models
• Phylogenetic Tree Visualization: allows the color-coded display of strain metadata on a tree using the Archaeopteryx viewer
• GBrowse: provides genome browsing capability for large DNA viral genomes with integration of ViPR Sequence Features for Vaccinia virus
• Sequence Feature Variant Type analysis: provides a centralized repository of functional regions and automatically calculates all observed sequence variation within each defined region
• 3D Protein Structure Visualization: integrates PDB protein structure files with ViPR Sequence Features when applicable and provides an interactive 3D protein structure viewer using Jmol
• Genome Annotator : allows users to annotate new genome sequences provided by the user
• Genotype Determination and Recombination Detection: predicts the genotype for user-provided sequences and identifies possible sites of recombination for viruses in the family Flaviviridae
• PCR Primer Design: allows the user to automatically predict ideal primers based on a sequence and specified parameters
• ReadSeq: converts between various sequence formats
• Sequence Feature Submission Tool: allows users to define a Sequence Feature by filling out a webform
• External Analysis Tools: displays a list and description of third-party tools for more specialized analyses
• Personal Workbench to save and share data and analysis