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A novel representation of DNA sequence based on CMI coding

Author

Listed:
  • Hou, Wenbing
  • Pan, Qiuhui
  • He, Mingfeng

Abstract

Graphical representation of DNA sequences provides a simple and intuitive way of analyzing and sorting various gene sequences. It is attractive to researchers to propose much more appropriate methods. In this study, a new graphical representation is presented. The method adopts the CMI coding to represent four nucleotides-A, G, C and T. Our approach considers not only the sequences’ structure but also the chemical structure for DNA sequence. We take several sets of data to test our method. The results of our experiment demonstrate that our representation is effective.

Suggested Citation

  • Hou, Wenbing & Pan, Qiuhui & He, Mingfeng, 2014. "A novel representation of DNA sequence based on CMI coding," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 409(C), pages 87-96.
    • Handle: RePEc:eee:phsmap:v:409:y:2014:i:c:p:87-96
    DOI: 10.1016/j.physa.2014.04.030
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    References listed on IDEAS

    as
    1. He, Ping-an & Wei, Jinzhou & Yao, Yuhua & Tie, Zhixin, 2012. "A novel graphical representation of proteins and its application," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 391(1), pages 93-99.
    2. Liao, Bo & Xiang, Qilin & Cai, Lijun & Cao, Zhi, 2013. "A new graphical coding of DNA sequence and its similarity calculation," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 392(19), pages 4663-4667.
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    Citations

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    Cited by:

    1. Jin, Xin & Nie, Rencan & Zhou, Dongming & Yao, Shaowen & Chen, Yanyan & Yu, Jiefu & Wang, Quan, 2016. "A novel DNA sequence similarity calculation based on simplified pulse-coupled neural network and Huffman coding," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 461(C), pages 325-338.
    2. Li, Yushuang & Liu, Qian & Zheng, Xiaoqi, 2016. "DUC-Curve, a highly compact 2D graphical representation of DNA sequences and its application in sequence alignment," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 456(C), pages 256-270.
    3. 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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