4.6 Article

Self-configuration single particle optimizer for DNA sequence compression

Journal

SOFT COMPUTING
Volume 17, Issue 4, Pages 675-682

Publisher

SPRINGER
DOI: 10.1007/s00500-012-0939-9

Keywords

DNA sequence compression; Particle swarm optimization; Self-configuration single particle optimizer; Compression codebook optimization

Funding

  1. National Natural Science Foundation of China [61171125, 61001185]
  2. NSFC-RS [61211130120]
  3. Fok Ying-Tung Education Foundation
  4. Guangdong Natural Science Foundation [10151806001000002]
  5. Foundation for Distinguished Young Talents in Higher Education of Guangdong [LYM10113]
  6. Scientific Research Foundation for the Returned Overseas Chinese Scholars
  7. Ministry of Education of China
  8. Science Foundation of Shenzhen City [JC201105170650A]
  9. Shenzhen City Foundation for Distinguished Young Scientists

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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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