Nucleic Acids Research Advance Access originally published online on April 27, 2008
Nucleic Acids Research 2008 36(Web Server issue):W35-W41; doi:10.1093/nar/gkn211
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Nucleic Acids Research, 2008, Vol. 36, No. suppl_2 W35-W41
© 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.
Articles |
PVS: a web server for protein sequence variability analysis tuned to facilitate conserved epitope discovery
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/.