Concurrent optimization in selection of primer and capture probe sets for nucleic acid analysis

Abstract

Disclosed is a method of iteratively optimizing two (or more) interrelated sets of probes for the multi-step analysis of sets of designated sequences, each such sequence requiring, for conversion, at least one conversion probe (“primer”), and each converted sequence requiring, for detection, at least one capture probe. The iterative method disclosed herein for the concurrent optimization of primer and probe selection invokes fast logical string matching functions to perform a complete cross-correlation of probe sequences and target sequences. The score function assigns to each probe-target alignment a “degree of matching” score on the basis of position-weighted Hamming distance functions introduced herein. Pairs of probes in the final selection may differ in several positions, while other pairs of probes may differ in only a single position. Not all such positions are of equal importance, and a score function is introduced, reflecting the position of the mismatch within the probe sequence.

1 . 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, 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; iteratively 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.   
     
     
         2 .- 55 . (canceled)