Patent ID: 8620589

Claim:
A system comprising: a memory for storing instructions and a computer programmed to execute the instructions stored in memory, such that the computer is programmed to perform the steps of: (a) using an initial restriction endonuclease or methyltransferase to query a database in a BLAST search, thereby creating a set of binding proteins wherein each binding protein has a defined amino acid sequence, the amino acid sequences sharing an expectation value (E) of less than e-20 for sequences of more than 200 amino acids or less than e-10 for sequences of less than 200 amino acids; the binding proteins binding to specific target recognition sequences in a substrate; (b) aligning the target recognition sequences recognized by the binding proteins in the set; (c) aligning the amino acid sequences of the binding proteins of the set; and (d) identifying correlations between single nucleotides the aligned recognition sequences and one or more position-specific amino acids in the aligned amino acid sequences of the binding proteins.