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Novel graphical representation of genome sequence and its applications in similarity analysis

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  • Yu, Hong-Jie
  • Huang, De-Shuang

Abstract

In order to compare different genome sequences, an alignment-free method has been proposed. Considering the essential property of sequence is sequentiality, we define a compound transformation which transforms a genome sequence into a sparse 16 by L−1 matrix M based on 16 kinds of 2-mer (dinucleotides). Furthermore, we found the transformation above-mentioned is an order-preserving transformation (OPT). Based on the theory of matrix analysis, we derive a 16-dimensional vector to characterize a genome sequence via singular value decomposition (SVD) of M. Finally, we analyze the similarities among multiple sequences from 20 eutherian species. The experiment results show that our approach performs well in the field of sequence analysis.

Suggested Citation

  • Yu, Hong-Jie & Huang, De-Shuang, 2012. "Novel graphical representation of genome sequence and its applications in similarity analysis," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 391(23), pages 6128-6136.
    • Handle: RePEc:eee:phsmap:v:391:y:2012:i:23:p:6128-6136
    DOI: 10.1016/j.physa.2012.07.020
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    Citations

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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.
    3. Ma, Tingting & Liu, Yuxin & Dai, Qi & Yao, Yuhua & He, Ping-an, 2014. "A graphical representation of protein based on a novel iterated function system," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 403(C), pages 21-28.

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