Normalized Lempel-Ziv complexity and its application in bio-sequence analysis

被引：24

作者：

Zhang, Yi ^{[1
]}

Hao, Junkang ^{[2
]}

Zhou, Changjie ^{[1
]}

Chang, Kai ^{[3
]}

机构：

[1] Hebei Univ Sci & Technol, Dept Math, Shijiazhuang 050018, HeBei, Peoples R China

[2] Hebei Univ Sci & Technol, Dept Phys Educ, Shijiazhuang 050018, HeBei, Peoples R China

[3] Beijing Inst Technol, Dept Automat Control, Sch Informat Sci & Technol, Beijing 100081, Peoples R China

来源：

JOURNAL OF MATHEMATICAL CHEMISTRY | 2009年 / 46卷 / 04期

关键词：

Lempel-Ziv complexity; Normalized; Similarity; Relationship tree; DNA PRIMARY SEQUENCES; RNA SECONDARY STRUCTURES; SIMILARITY ANALYSIS; GRAPHICAL REPRESENTATION;

D O I：

10.1007/s10910-008-9512-2

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

In this article, we propose a new method to measure DNA similarity based on a normalized Lempel-Ziv complexity scheme. The new method can weaken the effect of sequence length on complexity measurement and save computation time. Firstly, a DNA sequence is transformed into three (0,1)-sequences based on a scheme, which considers "A" and "non-A" , "G" and "non-G", "C" and "non-C" bases respectively. Then, the normalized Lempel-Ziv complexity of the three (0,1)-sequences constitute a 3D vector. Finally, by the 3D vector, one may characterize DNA sequences and compute similarity matrix for them. The examination of similarities of two sets of DNA sequences illustrates the utility of the method in local and global similarity analysis.

引用

页码：1203 / 1212

页数：10

共 17 条

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