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.
Received: 09 December 2008
Revised: 09 April 2009
Accepted manuscript online:
(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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