Confronting two-pair primer design using particle swarm optimization

Authors:
Cheng-Hong Yang;Yu-Huei Cheng;Li-Yeh Chuang
Affiliations:
Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan and Department of Network Systems, Toko University, Chiayi, Taiwan;Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan;Department of Chemical Engineering & Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung, Taiwan
Venue:
ICCCI'10 Proceedings of the Second international conference on Computational collective intelligence: technologies and applications - Volume Part III
Year:
2010

Citing 3
Cited 0

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Abstract

Polymerase chain reaction with confronting two-pair primers (PCRCTPP) is a novel PCR technique had been applied to many SNPs (Single Nucleotide Polymorphisms) genotyping experiments successfully in the recent years. The advantages of simplicity make it is a time- and cost-effective SNP genotyping method. However, computation of feasible CTPP primers is still challenging. In this study, a particle swarm optimization (PSO)-based method is proposed to design a feasible CTPP primer set. Overall, two hundred and eighty-eight SNPs in SLC6A4 gene were tested in silicon by the proposed method. The result indicates that the proposed method provide feasible CTPP primers effectively than the genetic algorithm (GA) in the literature. It can assist the biologists and researchers to obtain a feasible CTTP primer set.