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

Pickett, Brett E.; Sadat, Eva L.; Zhang, Yun; Noronha, Jyothi M.; Squires, R. Burke; Hunt, Victoria; Liu, Mengya; Kumar, Sanjeev; Zaremba, Sam; Gu, Zhiping; Zhou, Liwei; Larson, Christopher N.; Dietrich, Jonathan; Klem, Edward B.; Scheuermann, Richard H.

All sequence records in ViPR belonging to the designated taxon are searched to identify all unique amino acid sequence variations existing for a defined SF. Strains that repeat the same sequence variation pattern are assigned to the same 'Variant Type' (VT). All computed results are then stored in the database and can be accessed within ViPR. The Sequence Feature Details page displays additional information about the SF including the protein and strain from which it was originally identified, the observed VTs, hyperlinks to the homologous 3D protein structures, and the ability to search for a VT based on sequence. For simplicity, links to the relevant defined SFs and VTs are found on the respective Protein Details pages. By subdividing strains based on the unique sequence variations in defined protein regions, SFVT analysis can rapidly identify genotypic polymorphisms that correlate with a specific phenotype at a finer level of granularity than was previously possible.