Normalized Lempel-Ziv complexity and its application in bio-sequence analysis |
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| Authors: | Yi Zhang Junkang Hao Changjie Zhou Kai Chang |
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| Affiliation: | 1.Department of Mathematics,Hebei University of Science and Technology,Shijiazhuang,People’s Republic of China;2.Physical Education Department,Hebei University of Science and Technology,Shijiazhuang,People’s Republic of China;3.Department of Automatic Control, School of Information Science and Technology,Beijing Institute of Technology,Beijing,People’s Republic of China |
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| Abstract: | 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. |
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