T.B. Kurniawan, N.K. Khalid, Z. Ibrahim, M. Khalid (Malaysia), and M. Middendorf (Germany)
DNA Sequence Design, Ant Colony System (ACS), Thermodynamic.
Hybridization between a DNA sequence and its base pairing complement is crucial to retrieve the information stored in DNA sequences and operate a computation operation in DNA computing. Therefore, much works have focused on designing the DNA sequences to archive a reliable molecular computation and many algorithms have been proposed to obtain a set of good DNA sequences. In this paper, Ant Colony System (ACS) is proposed to solve the DNA sequence design problem. ACS as a derivate from Ant Colony Optimization (ACO) is an improvement from Ant System (AS) that used some agents to get their solutions based on the pheromone in their colony. A model is prepared which consists of four nodes representing four DNA bases using nearest neighbor thermodynamic parameter’s Watson-Crick base pair ΔGo 37 as the distance between nodes. The results of the proposed approach are compared with the other methods such as genetic algorithm and evolutionary algorithm.
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