Chaotic Inertia Weight Particle Swarm Optimization for PCR
Primer Design
Cheng-Huei Yang, Yu-Huei Cheng, Li-Yeh Chuang, Cheng-Hong Yang
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. Full Text
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