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Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines

Huynh-Hoa Bui12, John Sidney1, Wei Li1, Nicolas Fusseder1 and Alessandro Sette1*

Author Affiliations

1 La Jolla Institute for Allergy and Immunology, Division of Vaccine Discovery, 9420 Athena Circle, La Jolla, CA 92037, USA

2 Isis Pharmaceuticals, Inc., Antisense Drug Discovery, 1896 Rutherford Road, Carlsbad, CA 92008, USA

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BMC Bioinformatics 2007, 8:361  doi:10.1186/1471-2105-8-361

Published: 26 September 2007

Abstract

Background

In an epitope-based vaccine setting, the use of conserved epitopes would be expected to provide broader protection across multiple strains, or even species, than epitopes derived from highly variable genome regions. Conversely, in a diagnostic and disease monitoring setting, epitopes that are specific to a given pathogen strain, for example, can be used to monitor responses to that particular infectious strain. In both cases, concrete information pertaining to the degree of conservancy of the epitope(s) considered is crucial.

Results

To assist in the selection of epitopes with the desired degree of conservation, we have developed a new tool to determine the variability of epitopes within a given set of protein sequences. The tool was implemented as a component of the Immune Epitope Database and Analysis Resources (IEDB), and is directly accessible at http://tools.immuneepitope.org/tools/conservancy webcite.

Conclusion

An epitope conservancy analysis tool was developed to analyze the variability or conservation of epitopes. The tool is user friendly, and is expected to aid in the design of epitope-based vaccines and diagnostics.