Pso-based data clustering for DNA computing readout, implemented on lightcycler

Abstract

A Seven-Nodes Hamiltonian Path Problem (HPP) has been solved by Adleman in the first experiment of Deoxyribonucleic Acid (DNA) computation by using some biotechnology methods such as hybridization and polymerase chain reaction (PCR). Moreover, graduated PCR has been exploited to visualize the Hamiltonian path in that experiment. In this research, we have applied particle swarm optimization (PSO) for automation of DNA computing readout method based on real-time Polymerase Chain Reaction (PCR). Moreover, the aim of this automation is identifying two different reactions in real-time PCR which uses an approach that is combination of in vitro and in silico in order to inspect the placement of pairs of nodes in the Hamiltonian Path Problem (HPP). In addition, the real-time PCR experiment is implemented on LightCycler system and software by MATLAB is built to implement the PSO clustering.