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A new graphical coding of DNA sequence and its similarity calculation

Author

Listed:
  • Liao, Bo
  • Xiang, Qilin
  • Cai, Lijun
  • Cao, Zhi

Abstract

The DNA primary sequence is translated into “structure graph” based on classification of its four bases. Then the invariants, such as topological indices, are extracted from those graphic representations of DNA primary sequences, and used to calculate the similarities among the eleven species. From these similarities/dissimilarities the homologies can be revealed that they are in agreement with evolutionary relation satisfactorily.

Suggested Citation

  • 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.
    • Handle: RePEc:eee:phsmap:v:392:y:2013:i:19:p:4663-4667
    DOI: 10.1016/j.physa.2013.05.015
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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.
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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. 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.
    3. 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.
    4. 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.
    5. 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.

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