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Self-configuration single particle optimizer for DNA sequence compression

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Abstract

This paper presents a novel self-configuration single particle optimizer (SCSPO) for DNA sequence compression. Particularly, SCSPO searches an optimal compression codebook of all unique repeat patterns and then DNA sequences are compressed by replacing the duplicate fragments with the indexes of the corresponding matched code vectors in the codebook. Featured with a crucial self-configuration process, SCSPO optimizes the codebook with no predefined parameter settings required. Experimental results on benchmark numerical functions and real-world DNA sequences demonstrate that SCSPO is capable of attaining better fitness value than many other PSO variants and the proposed DNA sequence compression algorithm based on SCSPO attains encouraging compression performance.

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Acknowledgments

This work was supported partially by the National Natural Science Foundation of China, under Grants 61171125 and 61001185, the NSFC-RS joint project under grant 61211130120, the Fok Ying-Tung Education Foundation, Guangdong Natural Science Foundation, under Grants 10151806001000002, the Foundation for Distinguished Young Talents in Higher Education of Guangdong, under Grant LYM10113, Scientific Research Foundation for the Returned Overseas Chinese Scholars, Ministry of Education of China, the Science Foundation of Shenzhen City, under grant JC201105170650A, and the Shenzhen City Foundation for Distinguished Young Scientists.

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Authors and Affiliations

  1. College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, 518060, People’s Republic of China

    Zhen Ji & Zexuan Zhu

  2. College of Biomedical Engineering and Instrument Science, Zhejiang University, Zhejiang, 310027, People’s Republic of China

    Jiarui Zhou & Siping Chen

  3. School of Medicine, Shenzhen University, Shenzhen, 518060, People’s Republic of China

    Siping Chen

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  1. Zhen Ji
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  2. Jiarui Zhou
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Correspondence to Zhen Ji.

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Ji, Z., Zhou, J., Zhu, Z. et al. Self-configuration single particle optimizer for DNA sequence compression. Soft Comput 17, 675–682 (2013). https://doi.org/10.1007/s00500-012-0939-9

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  • DOI: https://doi.org/10.1007/s00500-012-0939-9

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