Patent ID: 8666670

Claim:
A method for determining a set, A, of double-stranded DNA sequences equal to or less than length L that are potential binding sites of a DNA-binding protein which has been exposed to a set of nucleic acid probes P, wherein jj is an index of said set P, subset B is the subset of probes of said set P to which said protein has bound, set T is the set of all possible nucleotide sequences of non-zero length and shorter or equal to length L and ii is an index of said set T, and where said set A is in an initially empty state, for each possible nucleotide sequence Tii, wherein set Hii is a corresponding initially empty set, the following steps are performed utilizing, at least in part, a digital computing device: a. comparing said sequence Tii to the sequence of each member, Pjj, of set P and: b1. if Tii is a subsequence of the sequence of Pjj; then, b2. adding Pjj to a set Hii of hypothetical probes corresponding to sequence Tii; c. determining if Hii is a subset of subset B; and, d. if the condition of step c is true, adding sequence Tii to said set A.