计算机科学 ›› 2020, Vol. 47 ›› Issue (11A): 192-195.doi: 10.11896/jsjkx.191200070
杜流云, 郑智捷, 郑华仙
DU Liu-yun, ZHENG Zhi-jie, ZHENG Hua-xian
摘要： 为了探索生物层次间的关系,从复杂细菌群落到各类种属细菌,全序列DNA测序蓬勃发展,对各种生物基因序列科学计算数据可视化的需求日益迫切。DNA序列双螺旋结构与空间复杂结构的互补对称性对于探索大量的长DNA序列具有重要意义。文中从“序列决定结构,结构决定功能”这一核心思想出发,基于一种基于变值体系的测量模型和方法,利用信息技术和统计学结合的方法对芽孢杆菌(Bacillus)和分枝杆菌(Mycobacterium)两类细菌的DNA全序列进行分析比较,展现了它们的DNA全序列二维特征分布,以可视化的形式显示这两类细菌的异同。与传统的细菌可视化方法相比,该方法具有时间复杂度低、稳定性好、直观性强、易于理解的特点。在不同的测量参考选择下提供了一系列分布图示。
中图分类号:
| [1] ZHU P X.Progress in microbial genome sequencing[J].Microorganisms and infection,1998(6):28-32. [2] SHI C,SUN Y,XIAO B,et al.Research on the discovery of new antibiotics by genome data mining[J].Journal of pharmacy,2018(6):845-851. [3] WANG J,GUO L,WU J S,et al.Current situation of bioinformatics research in the context of big data [J].Journal of Nanjing University of Posts and Telecommunications (Natural Science Edition),2017,37(4):62-67. [4] LV H Q,HAO L L,LIU E H,et al.Research status and development trend of Hi-C based on bioinformatics [J/OL].Genetics:1-14.[2019-12-05].Http://kns.cnki.net/kcms/detail/11.1913.r.20191127.1304.006.html. [5] WAN Z,ZHENG Z J E.Visualization of one-dimensional segmented measurement and distribution of DNA sequences [J].Journal of Yunnan University (Natural Science Edition),2013,35(S2). [6] LI C,LIU H,CHU W W,et al.Two dimensional graphical representation of DNA sequence and its application [J].Journal of Bohai University (Natural Science Edition),2014,35(4):307-312,324. [7] LI G L,RUAN Y,JGU R S,et al.Research on three-dimensional genomics [J].Science Bulletin,2014,59(13):1165-1172. [8] TANG X C,ZHOU P P,QIU W Y.DNA sequence similarity analysis based on 4D graphical representation [J].Science Bulletin,2010,55(6):442-446. [9] YANG C,YANG R F,CUI Y J,et al.Methods and applications of bacterial genome-wide association research[J].Genetics,2018,40(1):57-65. [10] LI C,LIU H,CHU W W,et al.Two dimensional graphical representation and application of DNA sequence non degradation [J].Journal of Bohai University (Natural Science Edition),2014,35(4):307-312,324. [11] ZHU T,ZENG D N,WHOLE P.Comparative analysis of bacterial community structure of skin between infant and mother[J].Microorganism and infection,2019,14(2):89. [12] ZHENG J.Variant Construction From Theoretical Foundation toApplications[M].Springer Singapore,2019:56. [13] JI Y.Research on Visualization Application of ECG data series based on VaR Measurement [D].Kunming:Yunnan University,2016. [14] LENG L H,ZHENG Z J.Visualization of ECG sequence of sinus arrhythmia [J].Computer Science,2016,43 (S2):183-185. [15] MAO Y,ZHENG J,LIU W.Mapping Whole DNA Sequence on Variant Maps[C]//IEEE/ACM International Conference.ACM,2017:1037-1040. |
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