Chaos Game Representation of Genomes and their Simulation by Recurrent Iterated Function Systems

Author

Yu, Zu-Guo ; Shi, Long ; Xiao, Qian-Jun ; Anh, Vo

Author_Institution

Sch. of Math. & Comput. Sci., Xiangtan Univ., Xiangtan

fYear

2008

Firstpage

41

Lastpage

46

Abstract

Chaos game representation (CGR) of DNA sequences and linked protein sequences from genomes was proposed by Jeffrey (Nucleic Acid Research 18 (1990) 2163-2170) and Yu et al. (J. Theor. Biol, 226 (2004) 341-348), respectively. In this paper, we consider the CGR of three kinds of sequences from complete genomes: whole genome DNA sequences, linked coding DNA sequences and linked protein sequences. Some fractal patterns are found in these CGRs. A recurrent iterated function systems (RIFS) model is proposed to simulate the CGRs of these sequences from genomes and their induced measures. Numerical results on 50 genomes show that the RIFS model can simulate very well the CGRs and their induced measures . The parameters estimated in the RIFS model reflect information on species classification .

Keywords

DNA; biological techniques; biology computing; fractals; genetics; molecular biophysics; proteins; chaos game representation; fractal patterns; genome DNA sequences; protein sequences; recurrent iterated function systems; Amino acids; Bioinformatics; Chaos; DNA; Fractals; Genomics; Magnetic field measurement; Proteins; Sequences; Visualization;

fLanguage

English

Publisher

ieee

Conference_Titel

Bioinformatics and Biomedical Engineering, 2008. ICBBE 2008. The 2nd International Conference on

Conference_Location

Shanghai

Print_ISBN

978-1-4244-1747-6

Electronic_ISBN

978-1-4244-1748-3

Type

conf

DOI

10.1109/ICBBE.2008.17

Filename

4534897