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Phylogenetic analysis of DNA sequences based on k-word and rough set theory

Author

Listed:
  • Li, Chun
  • Yang, Yan
  • Jia, Meiduo
  • Zhang, Yingying
  • Yu, Xiaoqing
  • Wang, Changzhong

Abstract

Among alignment-free methods for sequence comparison, the model of k-word frequencies is a well-developed one. However, most existing word-based methods neglect relationships among k-word frequencies, while a few others focus on the correlation of k-words but ignore the word frequency itself. In this paper, we propose a new k-word method which succeeds in conquering the two problems.

Suggested Citation

  • Li, Chun & Yang, Yan & Jia, Meiduo & Zhang, Yingying & Yu, Xiaoqing & Wang, Changzhong, 2014. "Phylogenetic analysis of DNA sequences based on k-word and rough set theory," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 398(C), pages 162-171.
    • Handle: RePEc:eee:phsmap:v:398:y:2014:i:c:p:162-171
    DOI: 10.1016/j.physa.2013.12.025
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    References listed on IDEAS

    as
    1. Li, Chun & Yu, Xiaoqing & Yang, Liu & Zheng, Xiaoqi & Wang, Zhifu, 2009. "3-D maps and coupling numbers for protein sequences," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 388(9), pages 1967-1972.
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    Cited by:

    1. Qian, Kun & Luan, Yihui, 2017. "Weighted measures based on maximizing deviation for alignment-free sequence comparison," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 481(C), pages 235-242.
    2. Qian, Kun & Luan, Yihui, 2018. "Phylogenetic analysis of DNA sequences based on fractional Fourier transform," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 509(C), pages 795-808.

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