Patent ID: 6963805

Claim:
A method for identifying a region as an evolutionarily conserved sequence, comprising the steps of: collecting a plurality of hybridization intensities wherein each of said intensities reflects the hybridization of one of a plurality of probes to a sample nucleic acid sequence from a first organism, wherein said probes are complementary and non-complementary to a known nucleic acid sequence from a second organism, wherein said probes are arrayed on a substrate and wherein each of said probes is at a known location on said substrate; identifying bases of said sample nucleic acid sequence according to said hybridization intensities; using said identified bases of said sample nucleic acid sequence and said known nucleic acid sequence to calculate a conformance between said known nucleic acid sequence and said sample nucleic acid sequence across said region of said sample nucleic acid sequence; measuring the distance from said region to the nearest repeat sequence; measuring the maximum single base frequency within said region; and measuring the maximum single base frequency in each of a set of subregions within said region, whereby if said conformance is at least 60%, said distance from said region to said nearest repeat sequence is more than 20 base pairs, said maximum single base frequency within said region is less than 50%, and said maximum single base frequency in each of said set of subregions within said region is less than 67%, said region is an evolutionarily conserved sequence.