A Novel Chaotic Inertia Weight Particle Swarm Optimization for PCR Primer Design

Many primer design methods have been proposed to provide feasible primer sets for performing polymerase chain reaction (PCR) experiments. However, the majority of these methods require a long time to obtain a feasible solution since large quantities of DNA template need to be analyzed and a specific PCR product size is not provided. Recently, particle swarm optimization (PSO) has been applied to solve many problems and yield good results. However, it is easily traped into a local optimal solution when the problem is complicated. In this paper, a novel logistic map is proposed to determine the value of inertia weight of PSO to design feasible primers (NCIWPSO). Accuracies for the primer design of the Homo sapiens RNA binding motif protein 11 (RBM11), mRNA (NM_144770), and the Homo sapiens G protein-coupled receptor 78 (GPR78), mRNA (NM_080819) were calculated. Five hundred runs of PSO and the NCIWPSO primer design methods performed different PCR product lengths with different melting temperature calculations. A comparison of the accuracies for PSO and the NCIWPSO primer design showed that the NCIWPSO is superior to PSO for primer design. The proposed method is effective for finding more feasible primer sets than PSO.