PVS: A Web Server for Protein Sequence Variability Analysis Tuned to Facilitate Conserved Epitope Discovery
Diez-Rivero, Carmen M.
Reche, Pedro A.
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CitationGarcia-Boronat, Maria, Carmen M. Diez-Rivero, Ellis L. Reinherz, and Pedro A. Reche. 2008. PVS: a web server for protein sequence variability analysis tuned to facilitate conserved epitope discovery. Nucleic Acids Research 36(Web Server issue): W35-W41.
AbstractWe have developed PVS (Protein Variability Server), 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. PVS is freely available at: http://imed.med.ucm.es/PVS/.
Citable link to this pagehttp://nrs.harvard.edu/urn-3:HUL.InstRepos:4875894
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