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Internet Electronic Journal of Molecular Design - IEJMD, ISSN 1538-6414, CODEN IEJMAT
ABSTRACT - Internet Electron. J. Mol. Des. January 2007, Volume 6, Number 1, 1-12

Similarity Analysis of DNA Sequences based on the LZ Complexity
Jia Wen and Chun Li
Internet Electron. J. Mol. Des. 2007, 6, 1-12

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Abstract:
Almost all methods for similarity analysis and phylogenetic inference are usually based on the multiple alignment of sequences or the invariants of sequences. But the former is not useful to all types of data, e.g. the whole genome comparisons, while the latter is accompanied by the complex calculation. The motivation of this paper is to introduce a new approach for similarity analysis of DNA sequences. We propose a relative distance measure of (0,1)-sequence based on the LZ complexity to quantify the similarity degree of two different binary sequences. By transforming a DNA sequence into three binary sequences in term of classifications of nucleic acid bases, we can obtain the relative distance of corresponding characteristic sequences of any two DNA sequences. The distance matrices are thus obtained to reflect the similarities of DNA sequences. A similarity comparison is made for the 24 complete coronavirus genomes to show the utility of our method. As a result, we find that the 24 complete coronavirus genomes can be classified into four groups on the whole. In particular, SARS-CoVs are not closely related to any of the previously characterized coronaviruses and form a distinct group within the genus coronaviruses. The result is consistent with those of previous analyses. On the basis of the findings, we conclude that the present method has apparently captured important features of DNA sequences considered and is useful for similarity analysis of DNA sequences.

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