基于拟南芥DNA序列的变值统计可视化分析
The Visual Analysis of Variables Statistic Based on Arabidopsis DNA Sequences

DOI: 10.12677/HJCB.2019.93006, PP. 39-47

Keywords: 拟南芥，DNA序列，变值图示，可视化
Arabidopsis, DNA Sequence, Variable Diagram, Visuali-zation

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Abstract:

随着植物基因组测序的展开，拟南芥基因测序因其巨大的科研价值得到了世界各国的重视。拟南芥基因序列的研究得到了极大的进展。由于传统的基因图示非常特殊和复杂，我们试图利用一种更为直观和普适的基因变值图示系统。利用该类模式，对从基因库获取到的DNA序列进行预处理后，统计碱基A，C，G，T的数量，计算AG，AT的数量，然后将数量投影到二维或者三维图像中，从而观察拟南芥的DNA序列的特征。从给出的系列图示可以看到，新的统计分布结果对后续为基因序列的相似性分析和更高维的特征研究提供基础信息。
With the development of plant genome sequencing, Arabidopsis gene sequencing has received great attention from all over the world for its great scientific research value. At the same time, the research on the sequence of Arabidopsis gene has been greatly advanced. Because of the specific and complex of traditional genetic representations, we try to use a more intuitive and universal genetic variable mapping system. Using this model, after preprocessing the DNA sequence obtained from the gene pool, we count the number of bases A, C, G, and T and calculate the number of AG, and AT. Then the quantity is projected into a two-dimensional or three-dimensional image which can observe the characteristics of the DNA sequence of Arabidopsis. As can be seen from the series of diagrams given, the new statistical distribution results provide basic information for subsequent similarity analysis of gene sequences and higher dimensional studies.

References

[1]	Zheng, J. (2018) Variant Construction from Theoretical Foundation to Applications. Springer, Berlin. https://doi.org/10.1007/978-981-13-2282-2
[2]	Hamori, E. and Ruskin, J. (1983) H Curves, a Novel Method of Representation of Nucleotide Series Especially Suited for Long DNA Sequences. The Journal of Biological Chemistry, 258, 1318-1327.
[3]	Gates, M.A. (1986) A Simple Way to Look at DNA. Journal of Theoretical Biology, 119, 319-328. https://doi.org/10.1016/S0022-5193(86)80144-8
[4]	Nandy, A. (1996) A New Graphical Representation and Analysis of DNA Sequence Structure I. Methodology and Application to Globin Genes. Current Science, 70, 611-668.
[5]	Leong, P.M. and Morgenthaler, S. (1995) Random Walk and Gap Plots of DNA Sequences. Computer Applications in the Biosciences, 11, 503-507. https://doi.org/10.1093/bioinformatics/11.5.503
[6]	Guo, X., Randic, M. and Basak, S.C. (2002) A Novel 2-D Graphical Representation of DNA Sequences of Low Degeneracy. Chemical Physics Letters, 350, 106-112. https://doi.org/10.1016/S0009-2614(01)01246-5
[7]	Wu, Y., Liew, A.W., Yan, H. and Yang, M. (2003) DB-Curve: A Novel 2D Method of DNA Sequence Visualization and Representation. Chemical Physics Letters, 367, 170-176. https://doi.org/10.1016/S0009-2614(02)01684-6
[8]	Yau, S.S.S., Wang, J., Niknejad, A., Lu, C., Jin, N. and Ho, Y. (2003) DNA Sequence Representation without Degeneracy. Nucleic Acid Research, 31, 3078-3080. https://doi.org/10.1093/nar/gkg432
[9]	https://www.arabidopsis.org/download/index-auto.jsp?dir=%2Fdownload_files%2FGenes%2FTAIR10_genome_release

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