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Issue No.03 - May-June (2012 vol.9)
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
ABSTRACT
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/.
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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