Chaos game representation walk model for the protein sequences

A new chaos game representation of protein sequences based on thedetailed hydrophobic--hydrophilic (HP) model has been proposed by Yuet al (Physica A 337 (2004) 171). A CGR-walk model isproposed based on the new CGR coordinates for the protein sequencesfrom complete genomes in the present paper. The new CGR coordinatesbased on the detailed HP model are converted into a time series, anda long-memory ARFIMA(p, d, q) model is introduced into theprotein sequence analysis. This model is applied to simulating realCGR-walk sequence data of twelve protein sequences. Remarkablylong-range correlations are uncovered in the data and the resultsobtained from these models are reasonably consistent with thoseavailable from the ARFIMA(p, d, q) model.