Universidad Complutense de Madrid
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PVS: a web server for protein sequence variability analysis tuned to facilitate conserved epitope discovery.

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García Boronat, María and Díez Rivero, Carmen M. and Reinherz, Ellis L and Reche, Pedro A (2008) PVS: a web server for protein sequence variability analysis tuned to facilitate conserved epitope discovery. Nucleic acids research, 36 (Web Se). W35-W41. ISSN 1362-4962

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Official URL: http://nar.oxfordjournals.org/content/36/suppl_2/W35.abstract



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/.


Item Type:Article
Subjects:Medical sciences > Medicine > Immunology
Medical sciences > Biology > Molecular biology
Sciences > Computer science > Bioinformatics
ID Code:9323
Deposited On:06 Aug 2009 07:45
Last Modified:13 Dec 2018 12:48

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