PVS -- Protein Variability Server

What you can do:
A web server for protein sequence variability analysis tuned to facilitate conserved epitope discovery.
Highlights:
  • PVS is a web-based tool that uses several variability metrics to compute the absolute site variability in multiple protein-sequence alignments (MSAs).
  • The variability is then assigned to a user-selected reference sequence consisting of either the first sequence in the alignment or a consensus sequence.
  • Subsequently, PVS performs tasks that are relevant for structure-function studies, such as plotting and visualizing the variability in a relevant 3D-structure.
  • Neatly, PVS also implements some other tasks that are thought to facilitate the design of epitope discovery-driven vaccines against pathogens where sequence variability largely contributes to immune evasion.
  • Thus, PVS can return the conserved fragments in the MSA-as defined by a user-provided variability threshold-and locate them in a relevant 3D-structure.
  • Furthermore, PVS can return a variability-masked sequence, which can be directly submitted to the RANKPEP server for the prediction of conserved T-cell epitopes.
Keywords:
  • multiple sequence alignment
  • protein sequence alignment
  • protein sequence variability
  • MSA
  • structure-function studies
This record last updated: 07-18-2008

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