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Confronting Two-Pair Primer Design Using Particle Swarm Optimization

  • Cheng-Hong Yang
  • Yu-Huei Cheng
  • Li-Yeh Chuang
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6423)

Abstract

Polymerase chain reaction with confronting two-pair primers (PCR-CTPP) 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.

Keywords

PCR-CTPP primer design PSO SNP 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Cheng-Hong Yang
    • 1
    • 2
  • Yu-Huei Cheng
    • 1
  • Li-Yeh Chuang
    • 3
  1. 1.Department of Electronic EngineeringNational Kaohsiung University of Applied SciencesKaohsiungTaiwan
  2. 2.Department of Network SystemsToko UniversityChiayiTaiwan
  3. 3.Department of Chemical Engineering & Institute of Biotechnology and Chemical EngineeringI-Shou UniversityKaohsiungTaiwan

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