A multiobjective swarm intelligence approach based on artificial bee colony for reliable DNA sequence design

Abstract

The design of reliable DNA sequences is crucial in many engineering applications which depend on DNA-based technologies, such as nanotechnology or DNA computing. In these cases, two of the most important properties that must be controlled to obtain reliable sequences are self-assembly and self-complementary hybridization. These processes have to be restricted to avoid undesirable reactions, because in the specific case of DNA computing, undesirable reactions usually lead to incorrect computations. Therefore, it is important to design robust sets of sequences which provide efficient and reliable computations. The design of reliable DNA sequences involves heterogeneous and conflicting design criteria that do not fit traditional optimization methods. In this paper, DNA sequence design has been formulated as a multiobjective optimization problem and a novel multiobjective approach based on swarm intelligence has been proposed to solve it. Specifically, a multiobjective version of the Artificial Bee Colony metaheuristics (MO-ABC) is developed to tackle the problem. MO-ABC takes in consideration six different conflicting design criteria to generate reliable DNA sequences that can be used for bio-molecular computing. Moreover, in order to verify the effectiveness of the novel multiobjective proposal, formal comparisons with the well-known multiobjective standard NSGA-II (fast non-dominated sorting genetic algorithm) were performed. After a detailed study, results indicate that our artificial swarm intelligence approach obtains satisfactory reliable DNA sequences. Two multiobjective indicators were used in order to compare the developed algorithms: hypervolume and set coverage. Finally, other relevant works published in the literature were also studied to validate our results. To this respect the conclusion that can be drawn is that the novel approach proposed in this paper obtains very promising DNA sequences that significantly surpass other results previously published.