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A novel genome signature based on inter-nucleotide distances profiles for visualization of metagenomic data

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  • Xie, Xian-Hua
  • Yu, Zu-Guo
  • Ma, Yuan-Lin
  • Han, Guo-Sheng
  • Anh, Vo

Abstract

There has been a growing interest in visualization of metagenomic data. The present study focuses on the visualization of metagenomic data using inter-nucleotide distances profile. We first convert the fragment sequences into inter-nucleotide distances profiles. Then we analyze these profiles by principal component analysis. Finally the principal components are used to obtain the 2-D scattered plot according to their source of species. We name our method as inter-nucleotide distances profiles (INP) method. Our method is evaluated on three benchmark data sets used in previous published papers. Our results demonstrate that the INP method is good, alternative and efficient for visualization of metagenomic data.

Suggested Citation

  • Xie, Xian-Hua & Yu, Zu-Guo & Ma, Yuan-Lin & Han, Guo-Sheng & Anh, Vo, 2017. "A novel genome signature based on inter-nucleotide distances profiles for visualization of metagenomic data," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 482(C), pages 87-94.
    • Handle: RePEc:eee:phsmap:v:482:y:2017:i:c:p:87-94
    DOI: 10.1016/j.physa.2017.04.064
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    References listed on IDEAS

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    1. Frédéric Guyon & Céline Brochier-Armanet & Alain Guénoche, 2009. "Comparison of alignment free string distances for complete genome phylogeny," Advances in Data Analysis and Classification, Springer;German Classification Society - Gesellschaft für Klassifikation (GfKl);Japanese Classification Society (JCS);Classification and Data Analysis Group of the Italian Statistical Society (CLADAG);International Federation of Classification Societies (IFCS), vol. 3(2), pages 95-108, September.
    2. Rachel Mackelprang & Mark P. Waldrop & Kristen M. DeAngelis & Maude M. David & Krystle L. Chavarria & Steven J. Blazewicz & Edward M. Rubin & Janet K. Jansson, 2011. "Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw," Nature, Nature, vol. 480(7377), pages 368-371, December.
    3. Möller, Simon & Hameister, Heike & Hütt, Marc-Thorsten, 2014. "A genome signature derived from the interplay of word frequencies and symbol correlations," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 414(C), pages 216-226.
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