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Mutagenic Primer Design for Mismatch PCR-RFLP SNP Genotyping Using a Genetic Algorithm
May-June 2012 (vol. 9 no. 3)
pp. 837-845
Cheng-Huei Yang, Dept. of Electron. Commun. Eng., Nat. Kaohsiung Marine Univ., Kaohsiung, Taiwan
Yu-Huei Cheng, Dept. of Network Syst., Toko Univ., Chiayi, Taiwan
Cheng-Hong Yang, Dept. of Network Syst., Toko Univ., Chiayi, Taiwan
Li-Yeh Chuang, Dept. of Chem. Eng., I-Shou Univ., Kaohsiung, Taiwan
Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) is useful in small-scale basic research studies of complex genetic diseases that are associated with single nucleotide polymorphism (SNP). Designing a feasible primer pair is an important work before performing PCR-RFLP for SNP genotyping. However, in many cases, restriction enzymes to discriminate the target SNP resulting in the primer design is not applicable. A mutagenic primer is introduced to solve this problem. GA-based Mismatch PCR-RFLP Primers Design (GAMPD) provides a method that uses a genetic algorithm to search for optimal mutagenic primers and available restriction enzymes from REBASE. In order to improve the efficiency of the proposed method, a mutagenic matrix is employed to judge whether a hypothetical mutagenic primer can discriminate the target SNP by digestion with available restriction enzymes. The available restriction enzymes for the target SNP are mined by the updated core of SNP-RFLPing. GAMPD has been used to simulate the SNPs in the human SLC6A4 gene under different parameter settings and compared with SNP Cutter for mismatch PCR-RFLP primer design. The in silico simulation of the proposed GAMPD program showed that it designs mismatch PCR-RFLP primers. The GAMPD program is implemented in JAVA and is freely available at http://bio.kuas.edu.tw/gampd/.

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Index Terms:
polymorphism,biochemistry,diseases,enzymes,genetic algorithms,genetics,molecular biophysics,GAMPD program,mutagenic primer design,mismatch PCR-RFLP SNP genotyping,genetic algorithm,polymerase chain reaction-restriction fragment length polymorphism,small-scale basic research,complex genetic diseases,single nucleotide polymorphism,feasible primer pair,restriction enzymes,optimal mutagenic primers,hypothetical mutagenic primer,human SLC6A4 gene,in silico simulation,JAVA,Biochemistry,Genetic algorithms,Annealing,Flowcharts,Genetics,Tides,Clamps,genetic algorithm (GA).,Polymerase chain reaction (PCR),restriction fragment length polymorphism (RFLP),single nucleotide polymorphism (SNP),mutagenic primer design
Citation:
Cheng-Huei Yang, Yu-Huei Cheng, Cheng-Hong Yang, Li-Yeh Chuang, "Mutagenic Primer Design for Mismatch PCR-RFLP SNP Genotyping Using a Genetic Algorithm," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, no. 3, pp. 837-845, May-June 2012, doi:10.1109/TCBB.2012.25
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