Chaotic Inertia Weight Particle Swarm Optimization for PCR Primer Design

Abstract

In order to provide feasible primer sets for performing a polymerase chain reaction (PCR) experiment, many primer design methods have been proposed. However, the majority of these methods require a long time to obtain an optimal solution since large quantities of template DNA need to be analyzed, and the designed primer sets usually do not provide a specific PCR product size. In recent years, particle swarm optimization (PSO) has been applied to solve many problems and yielded good results. In this paper, a logistic map is proposed to determine the value of inertia weight of PSO (CIWPSO) to design feasible primers. 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 CIWPSO primer design method were performed on different PCR product lengths and the different methods of calculating the melting temperature. A comparison of the accuracy results for PSO and CIWPSO primer design showed that CIWPSO is superior to the PSO for primer design. The proposed method could effectively find optimal or near-optimal primer sets.

Keywords

• Polymerase Chain Reaction (pcr)
• Primer Design
• Particle Swarm Optimization (pso)
• chaos