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Chin. Phys. B, 2009, Vol. 18(10): 4571-4579    DOI: 10.1088/1674-1056/18/10/079
CROSS DISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY Prev   Next  

Chaos game representation walk model for the protein sequences

Gao Jie(高洁)a)b)†, Jiang Li-Li(蒋丽丽)a), and Xu Zhen-Yuan(徐振源)a)
a School of Science, Jiangnan University, Wuxi 214122, China; b School of Information Technology, Jiangnan University, Wuxi 214122, China
Abstract  A new chaos game representation of protein sequences based on the detailed hydrophobic--hydrophilic (HP) model has been proposed by Yu et al (Physica A 337 (2004) 171). A CGR-walk model is proposed based on the new CGR coordinates for the protein sequences from complete genomes in the present paper. The new CGR coordinates based on the detailed HP model are converted into a time series, and a long-memory ARFIMA(p, d, q) model is introduced into the protein sequence analysis. This model is applied to simulating real CGR-walk sequence data of twelve protein sequences. Remarkably long-range correlations are uncovered in the data and the results obtained from these models are reasonably consistent with those available from the ARFIMA(p, d, q) model.
Keywords:  chaos game representation CGR-walk model       protein sequence      long-memory ARFIMA (p, d, q) model       autocorrelation function  
Received:  09 December 2008      Revised:  09 April 2009      Accepted manuscript online: 
PACS:  87.14.E- (Proteins)  
  05.40.Fb (Random walks and Levy flights)  
  87.15.A- (Theory, modeling, and computer simulation)  
  87.15.Cc (Folding: thermodynamics, statistical mechanics, models, and pathways)  
Fund: Project supported by the National Natural Science Foundation of China (Grant No 60575038), the Natural Science Foundation of Jiangnan University, China (Grant No 20070365) and the Program for Innovative Research Team of Jiangnan University, China.

Cite this article: 

Gao Jie(高洁), Jiang Li-Li(蒋丽丽), and Xu Zhen-Yuan(徐振源) Chaos game representation walk model for the protein sequences 2009 Chin. Phys. B 18 4571

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