Patent ID: 11862296
Assignee: NATIONAL KAOHSIUNG UNIVERSITY OF SCIENCE AND TECHNOLOGY
Field: Computer technology (Electrical engineering)
Classification: CPC G | IPC G

Claim 0:
1. A method for designing a multi-objective primer pair, comprising:
inputting a DNA template fragment, a length of a forward primer, a length of a reverse primer, at least two objectives and optimal values of each of the at least two objectives to a computer system;
generating, by the computer system, a plurality of primer pairs according to the DNA template fragment, the length of the forward primer and the length of the reverse primer; and
calculating, by the computer system, numerical values of the at least two objectives of each of the plurality of primer pairs and inputting the numerical values of the at least two objectives of each of the plurality of primer pairs to a Pareto Chart tool to determine at least one primer pair to be at least one optimal solution of the DNA template fragment;
wherein, in a circumstance that the at least one optimal solution is a single primer pair, each of the numerical values of the at least two objectives of the single primer pair of the at least one optimal solution dominates a respective one of the numerical values of the at least two objectives of the each of the others of the plurality of primer pairs;
wherein, in a circumstance that the at least one optimal solution is multiple primer pairs, the numerical values of the at least two objectives of each of the multiple primer pairs of the at least one optimal solution dominate each other, and each of the numerical values of the at least two objectives of multiple primer pairs of the at least one optimal solution dominates a respective one of the numerical values of the at least two objectives of each of the others of the plurality of primer pairs;
wherein, the at least two objectives include at least two of a first objective, a second objective, a third objective, a fourth objective, a fifth objective, a sixth objective, a seventh objective and an eighth objective, and one of the at least two objectives is the eighth objective;
wherein, the first objective is defined by a relationship between a melting temperature of a forward primer and a set optimal melting temperature of the forward primer;
wherein, the second objective is defined by a relationship between a melting temperature of a reverse primer and a set optimal melting temperature of the reverse primer;
wherein, the third objective is defined by a relationship among the melting temperature of the forward primer, the melting temperature of the reverse primer, the set optimal melting temperature of the forward primer and the set optimal melting temperature of the reverse primer;
wherein, the fourth objective is defined by a relationship on nucleotide types in 3′ ends of both the forward primer and the reverse primer;
wherein, the fifth objective is defined by a relationship between a proportion of ‘G’ and ‘C’ type nucleotides in the forward primer and a set optimal GC proportion of the forward primer;
wherein, the sixth objective is defined by a relationship between a proportion of ‘G’ and ‘C’ type nucleotides in the reverse primer and a set optimal GC proportion of the reverse primer;
wherein, under a circumstance that a plurality of forward primers and a plurality of reverse primers are provided and a polymerase chain reaction is carried out, the seventh objective is defined by a relationship among a quantity of bindings generated by the nucleotides of two forward primers of the plurality of forward primers, a quantity of bindings generated by the nucleotides of two reverse primers of the plurality of reverse primers, and a quantity of bindings generated by the nucleotides of one of the plurality of forward primers and one of the plurality of reverse primers; and
wherein, under the circumstance that the plurality of forward primers and the plurality of reverse primers are provided, and the polymerase chain reaction is carried out, the eighth objective is defined by:
calculating a quantity of self-annealings generated by the nucleotides of one forward primer of the plurality of forward primers to obtain a fourth quantity, wherein if the fourth quantity is not greater than a set optimal forward primer self-annealing quantity, a forward primer self-annealing quantity is equal to 0; if the fourth quantity is greater than the set optimal forward primer self-annealing quantity, the forward primer self-annealing quantity is equal to a difference between the fourth quantity and the set optimal forward primer self-annealing quantity;
calculating a quantity of self-annealings generated by the nucleotides of one reverse primer of the plurality of reverse primers to obtain a fifth quantity, wherein if the fifth quantity is not greater than a set optimal reverse primer self-annealing quantity, a reverse primer self-annealing quantity is equal to 0; if the fifth quantity is greater than the set optimal reverse primer self-annealing quantity, the reverse primer self-annealing quantity is equal to a difference between the fifth quantity and the set optimal reverse primer self-annealing quantity;
calculating a specificity of a primer pair formed by the forward primer and the reverse primer and multiplying by a set factor to obtain a specificity value; and
making the eighth objective equal to a sum of the forward primer self-annealing quantity, the reverse primer self-annealing quantity and the specificity value.