PCR-CTPP primer design using chaotic inertia weight particle swarm optimization

In this paper, a method named chaotic inertia weight particle swarm optimization (CIWPSO) for designing polymerase chain reaction experiments with confronting two-pair primers (PCR-CTPP) is proposed. PCR-CTPP is a time-and cost-effective technique for SNP (single nucleotide polymorphism) genotyping. In the past decades, many SNPs were genotyped successfully by it. However, computation of feasible CTPP primers is still in its fancy and challenging. In this study, we design PCR-CTPP primers in silico from 288 SNPs in the SLC6A4 gene by the proposed method. The results were compared with a PSO (particle swarm optimization) method and indicate that the proposed method improves the PSO to provide more feasible CTPP primers. The CIWPSO PCR-CTPP primer design method has the advantage of selecting a good melting temperature difference. It can assist researchers in obtaining feasible CTTP primer sets.