A method of epitope-based vaccine design

A method of epitope-based vaccine design comprising:

• providing target amino acid sequence(s) and annotation;
• a list of genomic features to be excluded from the result;
• a list of alleles which describe the population to be vaccinated;
• filtering peptides based on their antigenic score;
• filtering peptides based on their similarity with peptides from the population to be vaccinated, wherein optionally the peptides from the population to be vaccinated are wild-type peptides;
• filtering peptides based on a database of known genomic features;
• visualising the filtering process graphically in order to do quality control;
• for all the selected peptide lengths:
• predict immunogenic peptides for the immune system of the species targeted by the vaccine (for human vaccines, predict immunogenic MHC-I and MHC-II peptides) based on population structure;
• selecting peptides based on the p-value returned by the predictor;
• recombining peptides produced for different peptide lengths;
• generating statistics on:
• the number and lengths of peptides needed for each gene and the alleles in the population covered by each peptide;
• optionally selecting the peptides coming from “denser” genes in order to compact the construct;
• and
• assembling the peptides optionally with linkers.