| 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. |
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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 National
Natural Science Foundation of China (Grant No 60575038) and the
Natural Science Foundation of Jiangnan University, China (Grant No
20070365). |
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| 摘 要： | Chaos game representation (CGR) is an iterative mapping
technique that processes sequences of units, such as nucleotides in
a DNA sequence or amino acids in a protein, in order to determine
the coordinates of their positions in a continuous space. This
distribution of positions has two features: one is unique, and the
other is source sequence that can be recovered from the coordinates
so that the distance between positions may serve as a measure of
similarity between the corresponding sequences. A CGR-walk
model is proposed based on CGR coordinates for the DNA
sequences. The CGR coordinates are converted into a time
series, and a long-memory ARFIMA (p, d, q) model, where
ARFIMA stands for autoregressive fractionally integrated moving
average, is introduced into the DNA sequence analysis. This model is
applied to simulating real CGR-walk sequence data of ten
genomic sequences. Remarkably long-range correlations are uncovered
in the data, and the results from these models are reasonably fitted
with 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. |
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| Authors: | Gao Jie 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: | Chaos game representation (CGR) is an iterative mapping
technique that processes sequences of units, such as nucleotides in
a DNA sequence or amino acids in a protein, in order to determine
the coordinates of their positions in a continuous space. This
distribution of positions has two features: one is unique, and the
other is source sequence that can be recovered from the coordinates
so that the distance between positions may serve as a measure of
similarity between the corresponding sequences. A CGR-walk
model is proposed based on CGR coordinates for the DNA
sequences. The CGR coordinates are converted into a time
series, and a long-memory ARFIMA (p, d, q) model, where
ARFIMA stands for autoregressive fractionally integrated moving
average, is introduced into the DNA sequence analysis. This model is
applied to simulating real CGR-walk sequence data of ten
genomic sequences. Remarkably long-range correlations are uncovered
in the data, and the results from these models are reasonably fitted
with 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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