Figure 4

Sparse peptide sequence search. Examples of the two search types available in AntiJen: (Search 1) a substring query and (Searches 2 and 3) PROSITE-like sparse queries allowing sets of variable (indicated by asterisks) and alternative (encased in square brackets) amino acids in the search. In our example, each query is an extension of the previous search. The initial search type returns a single hit, which is a weak binder. By introducing variable amino acid positions within the query string, the second query permits access to a larger data set with 39 hits being returned. The third search utilises both variable and alternative amino acid request functionality and returns 1996 hits. The number of entries returned can be reduced by specifying the epitope length, limiting IC₅₀ values and restricting by one MHC allele. This search is constrained to peptides of amino acid length 9, which returns 280 hits. Constraining further by MHC allele HLA-A*0201, reduces this to 120. An additional constraint using the IC50 data filter, and requesting values below 500 only (the epitope range), reduces this again to 60.