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IWO Algorithm Based on Niche Crowding for DNA Sequence Design

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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.

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Acknowledgments

The authors would like to acknowledge the reviewers’ constructive suggestions and comments.

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Authors and Affiliations

  1. Key Laboratory of Advanced Design and Intelligent Computing (Dalian University), Ministry of Education, Dalian, 116622, China

    Gaijing Yang, Bin Wang, Xuedong Zheng, Changjun Zhou & Qiang Zhang

Authors
  1. Gaijing Yang
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  2. Bin Wang
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  3. Xuedong Zheng
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  4. Changjun Zhou
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  5. Qiang Zhang
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Correspondence to Qiang Zhang.

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Yang, G., Wang, B., Zheng, X. et al. IWO Algorithm Based on Niche Crowding for DNA Sequence Design. Interdiscip Sci Comput Life Sci 9, 341–349 (2017). https://doi.org/10.1007/s12539-016-0160-0

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  • DOI: https://doi.org/10.1007/s12539-016-0160-0

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