Patent ID: 7574305

Claim:
A method of optimizing the selection of a set of conversion probes and a set of detection probes, which together are used for the analysis of a set of nucleic acid sequences, wherein members of the set of conversion probes are complementary, in whole or in part, to cognate nucleic acid subsequences in the set of nucleic acid sequences and are used to generate conversion products by elongation of said conversion probes, and members of the set of detection probes are complementary, in whole or in part, to cognate target subsequences in the conversion products, comprising: establishing a first interaction matrix representing the sequence homologies of cognate nucleic acid subsequences to other subsequences in said set of nucleic acid sequences representing non-cognate alignments of the conversion probes with the nucleic acid sequences; establishing a second interaction matrix representing the sequence homologies of cognate target subsequences to other subsequences in said set of conversion products representing non-cognate alignments of the detection probes with the conversion products; optimizing the first and second interaction matrices so as to minimize the sequence homologies of cognate nucleic subsequences to said other subsequences in said set of nucleic acid sequences and to minimize the sequence homologies of cognate target subsequences to said other subsequences in said set of nucleic acid sequences; determining the set of conversion probes and the set of detection probes from said optimizing for use in said analysis of said set of nucleic acid sequences and outputting the set of conversion probes and the set of detection probes to a display; and using the set of detection probes to perform the analysis of the set of nucleic acid sequences in an assay wherein members of the set of detection probes interact with members of the set of nucleic acid sequences to form hybridization products, which are detected.