A method of making a hybridization probe the method comprising:
- receiving a target-specific hybridization sequence identified by:
- a) selecting a candidate target nucleotide sequence in a subject nucleotide sequence;
- b) identifying one or more interfering nucleotide sequences, wherein the interfering nucleotide sequences have at least a predetermined number of sequential nucleotides in common with the candidate target nucleotide sequence;
- c) identifying a first complementary nucleotide sequence to the target nucleotide sequence;
- d) determining a set of replacement positions Pn in the first complementary nucleotide sequence by locating each position at which a G is located;
- e) creating a set of second complementary nucleotide sequences by replacing each G at the replacement position with a nucleotide selected from the group consisting of T/U, C, and A, wherein each member of the set of second complementary nucleotide sequences has a single G replaced;
- f) characterizing the amount of “target-second complementary nucleotide sequence” hybrid formed when the target and second complementary nucleotide sequences are combined in the presence of potentially interfering sequences;
- g) identifying the second complementary nucleotide sequence as a symbolic representation of a target-specific hybridization sequence if the amount of “target-second complementary nucleotide sequence” hybrid is greater than a predetermined value;
- h) determining a set of replacement positions Pn in the first complementary nucleotide sequence by locating each position at which a C or A or T/U if the first complementary nucleotide sequence did not have a G or the amount of “target-second complementary nucleotide sequence” hybrid was not greater than the predetermined value;
- i) creating the set of second complementary nucleotide sequences by replacing C or A or T/U identified in step h) at the replacement position with a non-complementary nucleotide;
- j) characterizing the amount of “target-second complementary nucleotide sequence” hybrid formed when the target and second complementary nucleotide sequences are combined in the presence of potentially interfering sequences;
- and
- k) identifying the second complementary nucleotide sequence as the symbolic representation of a target specific hybridization sequence if the amount of “target-second complementary nucleotide sequence” hybrid is greater than a predetermined value, and generating an actual nucleotide sequence that is incorporated in the hybridization probe.