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Measure representation and multifractal analysis of complete genomes

Yu, Zu-Guo, Anh, Vo V., & Lau, Ka-Sing (2001) Measure representation and multifractal analysis of complete genomes. Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), 64(3), 031903.

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Abstract

This paper introduces the notion of measure representation of DNA sequences. Spectral analysis and multifractal analysis are then performed on the measure representations of a large number of complete genomes. The main aim of this paper is to discuss the multifractal property of the measure representation and the classification of bacteria. From the measure representations and the values of the Dq spectra and related Cq curves, it is concluded that these complete genomes are not random sequences. In fact, spectral analyses performed indicate that these measure representations, considered as time series, exhibit strong long-range correlation. Here the long-range correlation is for the K-strings with dictionary ordering, and it is different from the base pair correlations introduced by other people. For substrings with length K=8, the Dq spectra of all organisms studied are multifractal-like and sufficiently smooth for the Cq curves to be meaningful. With the decreasing value of K, the multifractality lessens. The Cq curves of all bacteria resemble a classical phase transition at a critical point. But the ‘‘analogous’’ phase transitions of chromosomes of nonbacteria organisms are different. Apart from chromosome 1 of C. elegans, they exhibit the shape of double-peaked specific heat function. A classification of genomes of bacteria by assigning to each sequence a point in two-dimensional space (D_{-1} ,D1) and in three-dimensional space (D_{-1} ,D1 ,D_{-2}) was given. Bacteria that are close phylogenetically are almost close in the spaces (D_{-1} ,D1) and (D_{-1} ,D1 ,D_{-2}).

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54 citations in Web of Science®

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204 since deposited on 06 Aug 2007
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ID Code: 7912
Item Type: Journal Article
Keywords: measure prepresentation, DNA, multifractal analysis
DOI: 10.1103/PhysRevE.64.031903
ISSN: 1550-2376
Subjects: Australian and New Zealand Standard Research Classification > PHYSICAL SCIENCES (020000) > OTHER PHYSICAL SCIENCES (029900) > Biological Physics (029901)
Australian and New Zealand Standard Research Classification > MATHEMATICAL SCIENCES (010000) > PURE MATHEMATICS (010100) > Ordinary Differential Equations Difference Equations and Dynamical Systems (010109)
Divisions: Past > QUT Faculties & Divisions > Faculty of Science and Technology
Current > Research Centres > Science Research Centre
Copyright Owner: Copyright 2001 The American Physical Society
Copyright Statement: Reproduced in accordance with the copyright policy of the publisher.
Deposited On: 06 Aug 2007
Last Modified: 11 Aug 2011 01:27

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