IWO Algorithm Based on Niche Crowding for DNA Sequence Design

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 d...

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Bibliographic Details
Published in:Interdisciplinary sciences : computational life sciences 2017-09, Vol.9 (3), p.341-349
Main Authors: Yang, Gaijing, Wang, Bin, Zheng, Xuedong, Zhou, Changjun, Zhang, Qiang
Format: Article
Language:English
Subjects:
Algorithms
Base Sequence
Biomedical and Life Sciences
Computational Biology/Bioinformatics
Computational Science and Engineering
Computer Appl. in Life Sciences
Computer Simulation
Computing time
Crowding
Deoxyribonucleic acid
Design
Dispersal
DNA
Fitness
Gene sequencing
Health Sciences
Life Sciences
Mathematical and Computational Physics
Medicine
Nucleotide sequence
Optimization
Original Research Article
Sequence Analysis, DNA
Statistics for Life Sciences
Theoretical
Theoretical and Computational Chemistry
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Summary: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.
ISSN:1913-2751
1867-1462
DOI:10.1007/s12539-016-0160-0