Three-unit semicircles curve: A compact 3D graphical representation of DNA sequences based on classifications of nucleotides

被引：8
|
作者：
Li, Yushuang [1 ]
Qin, Yufang [2 ]
Zheng, Xiaoqi [3 ,4 ,5 ]
Zhang, Yu
机构：
[1] Yanshan Univ, Sch Sci, Qinhuangdao 066004, Peoples R China
[2] Shanghai Ocean Univ, Coll Informat Technol, Shanghai 201306, Peoples R China
[3] Shanghai Normal Univ, Dept Math, Shanghai 200234, Peoples R China
[4] Sci Comp Key Lab Shanghai Univ, Shanghai 200234, Peoples R China
[5] Shijiazhuang Post & Telecommun Tech Coll, Dept Comp, Shijiazhuang 050021, Peoples R China
来源：
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY | 2012年 / 112卷 / 10期
基金：
中国国家自然科学基金;
关键词：
graphical representation; biclassification; invariant; similarity analysis; phylogenetic tree; H-CURVES; TOOL;
D O I：
10.1002/qua.23187
中图分类号：
O64 [物理化学（理论化学）、化学物理学];
学科分类号：
070304 ; 081704 ;
摘要：
A new three-dimensional graphical representation of DNA sequences, three-unit semicircles (TUS)-curve, which maps a given sequence into a dot sequences embedded in three-unit semicircles, is proposed based on three biclassifications of nucleotides. TUS-curve has the merit of compactness and could avoid the degeneracy and loss of information. The geometrical center of the curve, which indicates the distribution of base frequencies of the corresponding DNA sequence, is extracted and applied to analyze the similarity of various species. Phylogenetic tree of 11 species based on their first exons of beta-globin genes showed that the TUS-curve is a powerful tool to get valuable biological information. (c) 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
引用
收藏
页码：2330 / 2335
页数：6
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