Multiobjective Evolutionary Optimization of DNA Sequences for Reliable DNA Computing

作者：Sung‐Young Shin, In‐Hee Lee, Dongyung Kim, Byoung-Tak Zhang · 发表于：IEEE Transactions on Evolutionary Computation · 年份：2005 · DOI：10.1109/tevc.2005.844166 · 被引用次数：200 · 研究领域：DNA and Biological Computing、Advanced biosensing and bioanalysis techniques、DNA and Nucleic Acid Chemistry

DNA computing relies on biochemical reactions of DNA molecules and may result in incorrect or undesirable computations. Therefore, much work has focused on designing the DNA sequences to make the molecular computation more reliable. Sequence design involves with a number of heterogeneous and conflicting design criteria and traditional optimization methods may face difficulties. In this paper, we formulate the DNA sequence design as a multiobjective optimization problem and solve it using a constrained multiobjective evolutionary algorithm (EA). The method is implemented into the DNA sequence design system, NACST/Seq, with a suite of sequence-analysis tools to help choose the best solutions among many alternatives. The performance of NACST/Seq is compared with other sequence design methods, and analyzed on a traveling salesman problem solved by bio-lab experiments. Our experimental results show that the evolutionary sequence design by NACST/Seq outperforms in its reliability the existing sequence design techniques such as conventional EAs, simulated annealing, and specialized heuristic methods.