Measure representation and multifractal analysis of complete genomes
(2001) Measure representation and multifractal analysis of complete genomes. Physical Review E (Statistical, Nonlinear, and Soft Matter Physics) 64(3):031903.
Full text available as: |
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}).
| Item Type: | Journal Article |
|---|---|
| RM Number: | 0020021058 |
| Status: | Published |
| Keywords: | measure prepresentation; DNA; multifractal analysis |
| Subjects: | 240000 Physical Sciences > 249900 Other Physical Sciences > 249901 Biophysics 230000 Mathematical Sciences > 230100 Mathematics > 230113 Dynamical Systems |
| ID Code: | 7912 |
| Deposited By: | Yu, Zu-Guo |
| Deposited On: | 06 August 2007 |
| Alternative Locations: | http://dx.doi.org/10.1103/PhysRevE.64.031903 |
| Copyright Owner: | Copyright 2001 The American Physical Society |
| Copyright Statement: | Reproduced in accordance with the copyright policy of the publisher. |