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DUC-Curve, a highly compact 2D graphical representation of DNA sequences and its application in sequence alignment

Author

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  • Li, Yushuang
  • Liu, Qian
  • Zheng, Xiaoqi

Abstract

A highly compact and simple 2D graphical representation of DNA sequences, named DUC-Curve, is constructed through mapping four nucleotides to a unit circle with a cyclic order. DUC-Curve could directly detect nucleotide, di-nucleotide compositions and microsatellite structure from DNA sequences. Moreover, it also could be used for DNA sequence alignment. Taking geometric center vectors of DUC-Curves as sequence descriptor, we perform similarity analysis on the first exons of β-globin genes of 11 species, oncogene TP53 of 27 species and twenty-four Influenza A viruses, respectively. The obtained reasonable results illustrate that the proposed method is very effective in sequence comparison problems, and will at least play a complementary role in classification and clustering problems.

Suggested Citation

  • 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.
    • Handle: RePEc:eee:phsmap:v:456:y:2016:i:c:p:256-270
    DOI: 10.1016/j.physa.2016.03.061
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    References listed on IDEAS

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    4. 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.
    5. Ole Madsen & Mark Scally & Christophe J. Douady & Diana J. Kao & Ronald W. DeBry & Ronald Adkins & Heather M. Amrine & Michael J. Stanhope & Wilfried W. de Jong & Mark S. Springer, 2001. "Parallel adaptive radiations in two major clades of placental mammals," Nature, Nature, vol. 409(6820), pages 610-614, February.
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    Cited by:

    1. 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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