| Chaos game representation （CGR）-walk model for DNA sequences |
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| 引用本文： | 高洁,徐振源. Chaos game representation （CGR）-walk model for DNA sequences[J]. 中国物理 B, 2009, 18(1): 370-376. DOI: 10.1088/1674-1056/18/1/060 |
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| 作者姓名： | 高洁 徐振源 |
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| 作者单位： | (1)School of Science, Jiangnan University, Wuxi 214122, China;School of Information Technology, Jiangnan University,Wuxi 214122, China; (2)School of Science, Jiangnan University, Wuxi 214122, China |
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| 基金项目： | Project supported by the NationalNatural Science Foundation of China (Grant No 60575038) and theNatural Science Foundation of Jiangnan University, China (Grant No20070365). |
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| 摘 要： | Chaos game representation (CGR) is an iterative mappingtechnique that processes sequences of units, such as nucleotides ina DNA sequence or amino acids in a protein, in order to determinethe coordinates of their positions in a continuous space. Thisdistribution of positions has two features: one is unique, and theother is source sequence that can be recovered from the coordinatesso that the distance between positions may serve as a measure ofsimilarity between the corresponding sequences. A CGR-walkmodel is proposed based on CGR coordinates for the DNAsequences. The CGR coordinates are converted into a timeseries, and a long-memory ARFIMA (p, d, q) model, whereARFIMA stands for autoregressive fractionally integrated movingaverage, is introduced into the DNA sequence analysis. This model isapplied to simulating real CGR-walk sequence data of tengenomic sequences. Remarkably long-range correlations are uncoveredin the data, and the results from these models are reasonably fittedwith those from the ARFIMA (p, d, q) model.
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| 关 键 词： | CGR-walk model DNA sequence long-memory ARFIMA(p d q) model |
| 收稿时间： | 2008-04-24 |
Chaos game representation (CGR)-walk model for DNA sequences |
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| Gao Jie and Xu Zhen-Yuan. Chaos game representation (CGR)-walk model for DNA sequences[J]. Chinese Physics B, 2009, 18(1): 370-376. DOI: 10.1088/1674-1056/18/1/060 |
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| Authors: | Gao Jie and Xu Zhen-Yuan |
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| Affiliation: | School of Science, Jiangnan University, Wuxi 214122, China; School of Information Technology, Jiangnan University, Wuxi 214122, China |
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| Abstract: | Chaos game representation (CGR) is an iterative mappingtechnique that processes sequences of units, such as nucleotides ina DNA sequence or amino acids in a protein, in order to determinethe coordinates of their positions in a continuous space. Thisdistribution of positions has two features: one is unique, and theother is source sequence that can be recovered from the coordinatesso that the distance between positions may serve as a measure ofsimilarity between the corresponding sequences. A CGR-walkmodel is proposed based on CGR coordinates for the DNAsequences. The CGR coordinates are converted into a timeseries, and a long-memory ARFIMA (p, d, q) model, whereARFIMA stands for autoregressive fractionally integrated movingaverage, is introduced into the DNA sequence analysis. This model isapplied to simulating real CGR-walk sequence data of tengenomic sequences. Remarkably long-range correlations are uncoveredin the data, and the results from these models are reasonably fittedwith those from the ARFIMA (p, d, q) model. |
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| Keywords: | CGR-walk model DNA sequence long-memory ARFIMA(p d q) model |
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