title: IWO Algorithm Based on Niche Crowding for DNA Sequence Design.
abstract: The design of DNA sequences is essential for the implementation of DNA computing, where the quantity and quality can directly affect the accuracy and efficiency of calculations. Many studies have focused on the design of good DNA sequences to make DNA computing more reliable. However, DNA sequence design needs to satisfy various constraints at the same time, which is an NP-hard problem. In this study, we specify appropriate constraints that should be satisfied in the design of DNA sequences and we propose evaluation formulae. We employ the Invasive Weed Optimization (IWO) algorithm and the niche crowding in the algorithm to solve the DNA sequence design problem. We also improve the spatial dispersal in the traditional IWO algorithm. Finally, we compared the sequences obtained with existing sequences based on the results obtained using a comprehensive fitness function, which demonstrated the efficiency of the proposed method.
authors.affiliation: Key Laboratory of Advanced Design and Intelligent Computing (Dalian University), Ministry of Education, Dalian, 116622, China.
authors.forename: Gaijing
authors.initials: G
authors.lastname: Yang
authors.affiliation: Key Laboratory of Advanced Design and Intelligent Computing (Dalian University), Ministry of Education, Dalian, 116622, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Wang
authors.affiliation: Key Laboratory of Advanced Design and Intelligent Computing (Dalian University), Ministry of Education, Dalian, 116622, China.
authors.forename: Xuedong
authors.initials: X
authors.lastname: Zheng
authors.affiliation: Key Laboratory of Advanced Design and Intelligent Computing (Dalian University), Ministry of Education, Dalian, 116622, China.
authors.forename: Changjun
authors.initials: C
authors.lastname: Zhou
authors.affiliation: Key Laboratory of Advanced Design and Intelligent Computing (Dalian University), Ministry of Education, Dalian, 116622, China. zhangq30@yahoo.com.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Zhang
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D003198:Computer Simulation; D017422:Sequence Analysis, DNA
keywords: DNA computing; DNA sequence design; Invasive Weed Optimization algorithm; Niche crowding