PVS: A Web Server for Protein Sequence Variability Analysis Tuned to Facilitate Conserved Epitope Discovery
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PVS: A Web Server for Protein Sequence Variability Analysis Tuned to Facilitate Conserved Epitope Discovery
| Title: | PVS: A Web Server for Protein Sequence Variability Analysis Tuned to Facilitate Conserved Epitope Discovery |
| Author: |
Garcia-Boronat, Maria; Diez-Rivero, Carmen M.; Reche, Pedro A.; Reinherz, Ellis Leonard
Note: Order does not necessarily reflect citation order of authors. |
| Citation: | Garcia-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. |
| Full Text & Related Files: |
2447719.pdf (407.4Kb; PDF) 
|
| Abstract: | We 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/. |
| Published Version: | doi:10.1093/nar/gkn211 |
| Other Sources: | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447719/pdf/ |
| Terms of Use: | This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA |
| Citable link to this page: | http://nrs.harvard.edu/urn-3:HUL.InstRepos:4875894 |
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