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Research Article
Visualizations of Combinatorial Entropy Index on Whole SARS-CoV-2 Genomes
Jeffrey Zheng
Yunnan University
Corresponding Author
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This work is licensed under a CC BY 4.0 License. Read Full License
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Declarations
- The author has confirmed that a statement listing potential conflicts of interest or lack thereof is included in the text.
In this paper, a set of SARS-CoV-2 genomes from four countries are selected for visualizations under the C1 modules of the metagenomic analysis system MAS. Based on the variant construction and the theory of information entropy, the module makes statistics on the number of bases in SARS-CoV-2 sequences to calculate the base probability measures in segments to generate the combinatorial entropy index data from the base probability measures. Under visualization technology, the combinatorial entropy index is projected on 2D clustering genomic index maps and 1D histogram maps to provide projection results. The visual results provide intuitive and easy properties to analyze complicated clustering among genomes to support clustering analysis of SARS-CoV-2 genomes in batches, showing the distribution characteristics of SARS-CoV-2 genomes in different countries or regions conveniently.
Keywords
metagenomic analysis system MAS, combinatorial entropy, variant construction, genomic index, geometric visualization
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This is a preprint. It has not completed peer review.
Research Article
Visualizations of Combinatorial Entropy Index on Whole SARS-CoV-2 Genomes
Jeffrey Zheng
Yunnan University
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
Version 2
Posted 08 Jan, 2021
No community comments so far
No comments provided
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Declarations:
Declarations
- The author has confirmed that a statement listing potential conflicts of interest or lack thereof is included in the text.
In this paper, a set of SARS-CoV-2 genomes from four countries are selected for visualizations under the C1 modules of the metagenomic analysis system MAS. Based on the variant construction and the theory of information entropy, the module makes statistics on the number of bases in SARS-CoV-2 sequences to calculate the base probability measures in segments to generate the combinatorial entropy index data from the base probability measures. Under visualization technology, the combinatorial entropy index is projected on 2D clustering genomic index maps and 1D histogram maps to provide projection results. The visual results provide intuitive and easy properties to analyze complicated clustering among genomes to support clustering analysis of SARS-CoV-2 genomes in batches, showing the distribution characteristics of SARS-CoV-2 genomes in different countries or regions conveniently.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8
Figure 9
Figure 10
Figure 11
Figure 12
Figure 13
Figure 14
Figure 15
Due to technical limitations, full-text HTML conversion of this manuscript could not be completed. However, the manuscript can be downloaded and accessed as a PDF.