Fig. 1.

(A) Input parameters for EpIC. Two sets of parameters are required for analysis: the target sequence information and the desired presentation of the epitope in the final immunizing antigen. The above figure demonstrates the input parameters for our example prion epitope. The target protein sequence is sheep PRNP and our site-specific minimal target sequence (or core sequence) is YML, in green. EpIC enables the user to customize the presentation of the optimized epitope by inserting a linker sequence, including a repeat pattern with presentation of each repeat as forward or reverse, and the desired expansion of the core epitope can be restricted by defining a min/max. For our purposes, the most immunogenic format involved a forward, reverse, reverse presentation repeated four times with short linker sequences between the repeats. EpIC performs the immunogenicity analysis by converting the epitope expansion to the desired presentation pattern, as these features affect the overall immunogenicity of the immunizing antigen. (B) Analysis of core epitope YML using EpIC. The top five ranking epitopes based on average prediction scores are illustrated. The immunogenic YML expansion identified previously is outlined in blue