Dimensions of fractals related to languages defined by tagged strings in complete genomes

DOI10.1016/S0960-0779(99)00141-1zbMATH Open0980.92026arXivphysics/9910040OpenAlexW3105979210MaRDI QIDQ1581740FDOQ1581740

Authors: Huimin Xie, Guoyi Chen, Zu-Guo Yu, Bailin Hao 

Publication date: 8 October 2000

Published in: Chaos, Solitons and Fractals (Search for Journal in Brave)

Abstract: A representation of frequency of strings of length K in complete genomes of many organisms in a square has led to seemingly self-similar patterns when K increases. These patterns are caused by under-represented strings with a certain "tag"-string and they define some fractals when K tends to infinite. The Box and Hausdorff dimensions of the limit set are discussed. Although the method proposed by Mauldin and Williams to calculate Box and Hausdorff dimension is valid in our case, a different and simpler method is proposed in this paper.

Full work available at URL: https://arxiv.org/abs/physics/9910040

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zbMATH Keywords

DNA sequenceHausdorff dimensionsBox dimension

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Fractals (28A80)

Cites Work

• Title not available (Why is that?)
• Hausdorff Dimension in Graph Directed Constructions
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• Fractals related to long DNA sequences and complete genomes
• The Goulden—Jackson cluster method: extensions, applications and implementations
• An Inversion Theorem for Cluster Decompositions of Sequences with Distinguished Subsequences
• Grammatical Complexity and One-Dimensional Dynamical Systems

Cited In (15)

• Multifractal characterisation of length sequences of coding and noncoding segments in a complete genome
• A time series model of CDS sequences in complete genome
• Multifractal properties of Hao's geometric representations of DNA sequences
• The genomic tree of living organisms based on a fractal model
• Self-similar fractals with a given dimension and the application to quantitative linguistics
• Chaos game representation of protein sequences based on the detailed HP model and their multifractal and correlation analyses
• Fractal properties of the human genome
• The fractal structure of the mitochondrial genomes
• Analysis of DNA chains by means of factorial moments
• Fourier transform and mean quadratic variation of Bernoulli convolution on homogeneous Cantor set
• Distance, correlation and mutual information among portraits of organisms based on complete genomes
• ON THE VISUALIZATION OF STRINGS AND FRACTALS OF SOME FORBIDDEN WORDS
• A NOTE ON FRACTALS OF ONE FORBIDDEN WORD AND THEIR BOX DIMENSIONS
• Time series model based on global structure of complete genome
• Fractal-based analysis of sign language

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