Patent ID: 7013221
Filing Date: 2006-03-14
Classification: G16B

Abstract:
1. A method for selecting one or more different polynucleotide probes from a plurality of different polynucleotide probes of different nucleotide sequence according to the sensitivity and specificity with which each different polynucleotide probe hybridizes to a target polynucleotide, said method comprising: (a) identifying polynucleotide probes in the plurality of different polynucleotide probes that hybridize to the target polynucleotide with a sensitivity above a threshold sensitivity level; (b) ranking the identified polynucleotide probes according to the specificity with which each identified polynucleotide probe hybridizes to the target polynucleotide, wherein the specificity of a probe is represented by a quantity selected from the group consisting of (i) a ratio of target polynucleotide molecules to non-target polynucleotide molecules hybridized to said probe under a particular set of hybridization conditions and (ii) a cross-hybridization score based on calculated binding energies of said probe to non-target polynucleotide molecules, wherein said target polynucleotide molecules hybridize with said probe with perfect match, and wherein said non-target polynucleotide molecules hybridize with said probe with one or more mismatches; and (c) selecting one or more different polynucleotide probes from the ranked polynucleotide probes.