Generate all possible peptide epitopes from a group of proteins

T-cell epitopes range in size between 9 and 15 AA. To test, for example, all possible 12mers in a set of proteins, becomes quickly unfeasible because of the high numbers. Here we use the fact, that, for example, a 20mer peptide can cover up to 9 different 12mers. We therefore use a combinatorial approach to cover all possible 12mers represented in a family of proteins. Lets define the length of peptides to generate as L (e.g. 20) and the length of the epitopes we want to cover as S. In a computer program we can easily generate all uniquely occurring Lmers from a set of proteins. We can also generate all uniquely occurring Smers from this set of proteins. Further for a list of N Lmers it can be tested, whether all unique Smers are covered.