Patent ID: 7739055

Claim:
A method of identifying antimicrobial peptides comprising: (a) providing a database of known antimicrobial peptides, (b) defining a set of integer parameters comprising L, W and K, wherein L is the minimum number of characters that may define a pattern, wherein L/W is the minimum density of non-wild card characters over a window of W characters, and wherein K is the minimum number of times a pattern occurs in the database, (c) screening the database with an algorithm that discovers all grammars in the database of antimicrobial peptides by applying integer parameters L=6, W=6, and K=2, (d) masking the resulting grammars from the input sequences, (e) repeating the algorithm with L=7, W=15, and K=5 with the amino acid equivalency group [[AG], [DE], [FYW], [KR], [ILMV], [QN], [ST]], (f) dividing all grammars to sliding windows of ten amino acids, (g) filtering grammars for selectivity by eliminating grammars that are not 80% selective for antimicrobial peptides in a database of known antimicrobial peptides from AMSdb and known antimicrobial peptides from Swiss-Prot/TrEMBL, (h) enumerating all 20 amino acid sequences which are matched over every sliding window of 10 amino acids by at least one grammar, (i) scoring the enumerated sequences against the grammars of step (g), and selecting relatively high scoring sequences for synthesizing and testing, and (j) testing the synthesized sequences for antimicrobial activity.