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Tetrahedral Gray Code for Visualization of Genome Information

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  • Natsuhiro Ichinose
  • Tetsushi Yada
  • Osamu Gotoh

Abstract

We propose a tetrahedral Gray code that facilitates visualization of genome information on the surfaces of a tetrahedron, where the relative abundance of each -mer in the genomic sequence is represented by a color of the corresponding cell of a triangular lattice. For biological significance, the code is designed such that the -mers corresponding to any adjacent pair of cells differ from each other by only one nucleotide. We present a simple procedure to draw such a pattern on the development surfaces of a tetrahedron. The thus constructed tetrahedral Gray code can demonstrate evolutionary conservation and variation of the genome information of many organisms at a glance. We also apply the tetrahedral Gray code to the honey bee (Apis mellifera) genome to analyze its methylation structure. The results indicate that the honey bee genome exhibits CpG overrepresentation in spite of its methylation ability and that two conserved motifs, CTCGAG and CGCGCG, in the unmethylated regions are responsible for the overrepresentation of CpG.

Suggested Citation

  • Natsuhiro Ichinose & Tetsushi Yada & Osamu Gotoh, 2014. "Tetrahedral Gray Code for Visualization of Genome Information," PLOS ONE, Public Library of Science, vol. 9(1), pages 1-10, January.
    • Handle: RePEc:plo:pone00:0086133
    DOI: 10.1371/journal.pone.0086133
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    References listed on IDEAS

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    1. Gutiérrez, J.M. & Rodrı́guez, M.A. & Abramson, G., 2001. "Multifractal analysis of DNA sequences using a novel chaos-game representation," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 300(1), pages 271-284.
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