An Ant Colony System for DNA Sequence Design based on Thermodynamics

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.

Important Links:

Go Back