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Nucleic Acids Research Advance Access published online on April 27, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn211
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Web Server

PVS: a web server for protein sequence variability analysis tuned to facilitate conserved epitope discovery

Maria Garcia-Boronat1, Carmen M. Diez-Rivero1, Ellis L. Reinherz2,3 and Pedro A. Reche1,*

1Immunomedicine Group, Department of Microbiology I, Division of Immunology, Facultad de Medicina, Universidad Complutense de Madrid, Ave Complutense s/n, Madrid 28040, Spain, 2Laboratory of Immunobiology and Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine and 3Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA

*To whom correspondence should be addressed. Tel: +34 91 394 7229; Fax: +34 91 394 1641; Email: parecheg{at}med.ucm.es

Received January 20, 2008. Revised April 3, 2008. Accepted April 9, 2008.

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/.


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