Patent ID: 7344831
Filing Date: 2008-03-18
Classification: C12Q

Abstract:
1. A method for analyzing a target nucleic acid sequence, said method comprising: (a) identifying a cross-hybridization oligonucleotide probe based on a candidate target-specific oligonucleotide probe for said target nucleic acid sequence wherein said cross-hybridization oligonucleotide probe measures the extent of the occurrence of a cross-hybridization event having a predetermined probability and wherein said identifying is carried out by a process comprising deleting or inserting nucleotides at one or more positions in a cross-hybridization oligonucleotide probe or by a process comprising a combination of (i) deleting nucleotides at one or more first positions in a cross-hybridization oligonucleotide probe and substituting nucleotides at one or more second positions in the cross-hybridization oligonucleotide probe, or (ii) deleting nucleotides at one or more first positions in a cross-hybridization oligonucleotide probe and inserting nucleotides at one or more second positions in the cross-hybridization oligonucleotide probe, or (iii) inserting nucleotides at one or more first positions in a cross-hybridization oligonucleotide probe and substituting nucleotides at one or more second positions in the cross-hybridization oligonucleotide probe, (b) determining cross-hybridization results employing said cross-hybridization oligonucleotide probe and said candidate target-specific oligonucleotide probe and including or not including said candidate target-specific oligonucleotide probe in a set of target specific oligonucleotide probes for said target nucleic acid sequence based on said cross-hybridization results, (c) contacting said set of target-specific oligonucleotide probes with a sample suspected of containing a target nucleic acid sequence, and (d) determining the extent of hybridization of said target-specific oligonucleotide probes to said target nucleic acid sequence.