Patent ID: 8234079

Claim:
A method of designing at least one oligonucleotide for nucleic acid detection comprising the following steps in any order: (I) computing an amplification efficiency score (AES i ) for every position i of a target nucleic acid v a : AES i = ∑ j = i - Z i ⁢ ⁢ { P f ⁡ ( j ) × ∑ k = max ⁡ ( i + 1 , j + 500 ) j + Z ⁢ ⁢ P r ⁡ ( k ) } wherein ∑ k = max ⁡ ( i + 1 , j + 500 ) j + Z ⁢ ⁢ P r ⁡ ( k ) = P r ⁡ ( i + 1 ) + P r ⁡ ( i + 2 ) + … ⁢ ⁢ P r ⁡ ( j + Z ) ; P f (i) and P r (i) are the probabilities that a random primer r i binds to position i of v a as forward random primer and reverse random primer respectively, and Z≦10000 bp is the region of v a desired to be amplified; (II) identifying and/or selecting at least one region of at least one target nucleic acid to be amplified, the region(s) having an efficiency of amplification (AE) higher than the average AE; and (III) designing at least one oligonucleotide capable of hybridizing to the identified and/or selected region(s), wherein the method is implemented by a computing processing unit.