Patent ID: 7144699

Claim:
A method of analyzing a target nucleic acid, comprising: (a) designing an array of probes based on a known reference sequence, the array comprising a probe set comprising probes complementary to and spanning the known reference sequence, the probes immobilized on at least one support; (b) hybridizing the target nucleic acid to the array of probes, wherein the target nucleic acid has a sequence which is a variant of the reference sequence and provided the array of probes does not contain every possible probe sequence of a given length; (c) determining the relative hybridization of the probes to the target nucleic acid, (d) estimating the sequence of the target nucleic acid from the relative hybridization of the probes; (e) designing a further array of probes based on the estimated sequence obtained in step (d), the further array comprising a probe set comprising probes complementary to and spanning the estimated sequence of the target nucleic acid, the probes immobilized on at least one support and provided the further probe array does not contain every possible probe sequence of a given length; (f) hybridizing the target nucleic acid to the further array of probes; (g) determining the relative hybridization of the probes of the further array to the target nucleic acid; (h) reestimating the sequence of the target nucleic acid from the relative hybridization of the probes of the further array.