Chaos game representation walk model for the protein sequences |
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Authors: | Gao Jie Jiang Li-Li and Xu Zhen-Yuan |
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Institution: | School of Science, Jiangnan University, Wuxi 214122, China; School of Information Technology, Jiangnan University, Wuxi 214122, China |
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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. |
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Keywords: | chaos game representation
CGR-walk model protein sequence long-memory ARFIMA (p d q) model autocorrelation function |
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