Patent ID: 7657382

Claim:
A method of designing primer and probe sets for identification of a target sequence by amplification and hybridization, comprising: (a) preparing a subsequence set for each target sequence in a plurality of target sequences, wherein a subsequence set for a target sequence is prepared by cleaving the target sequence into subsequences meeting a predetermined criterion wherein each base pair (bp) of the target sequence is a start site for a subsequence meeting the predetermined criterion; (b) comparing the subsequence sets pairwise for homology greater than or equal to a predetermined level to determine a number of subsequences in each pair of subsequence sets having homology greater than or equal to the predetermined level; (c) selecting the pair of subsequence sets for which the number of subsequences having homology greater than the predetermined level is greatest among all the subsequence sets; (d) selecting subsequences which have homology greater than the predetermined level in the selected pair of subsequence sets as a common subsequence set for the selected pair of subsequence sets and selecting the remaining subsequences in the selected pair of subsequence sets as probes for the selected pair of subsequence sets; (e) replacing the selected pair of subsequence sets with the common subsequence set for the selected pair of subsequence sets; (f) performing operations (b) to (e) on pairs of subsequence sets consisting of unselected subsequence sets and common subsequence sets until there is only one common subsequence set remaining or there are no subsequences having homology greater than or equal to the predetermined level between any pairs of subsequence sets remaining; and (g) selecting subsequences of remaining subsequence sets as primers for the plurality of target sequences, wherein the method is executed by a suitably-programmed computer.