Epitope Conservancy Tool Description

The Epitope Conservancy Tool can be found at http://tools.immuneepitope.org/main/html/analysis_tools.html.

In a diagnostic or epitope-based vaccine setting, focusing on conserved epitopes allows for targeting responses around pathogen variability, whether it exists prior to infection, or develops in the natural course of disease.  The use of conserved epitopes would be expected to focus the immune response on sequences crucial for retaining biological function of the pathogen proteins, and thus with intrinsically lower variability, even under immune pressure. The epitope conservancy analysis tools implemented here aims to address the issue of variability (or conservation) of epitopes, and to assist in the selection of epitopes with the desired pattern of conservation.  The algorithm has been implemented to calculate the degree of conservancy of an epitope within a given protein sequence set at different degree of identities. The degree of conservation is defined as the number of protein sequences that contain the epitope at a given identity level, divided by the total number of protein sequences found in the dataset analyzed (Bui et al. BMC Bioinformatics 2007).