A generalized topological entropy for analyzing the complexity of DNA sequences

Shuilin Jin; Renjie Tan; Qinghua Jiang; Li Xu; Jiajie Peng; Yong Wang; Yadong Wang

doi:10.1371/journal.pone.0088519

A generalized topological entropy for analyzing the complexity of DNA sequences

Shuilin Jin, Renjie Tan, Qinghua Jiang, Li Xu, Jiajie Peng, Yong Wang, Yadong Wang

Research output: Contribution to journal › Article › peer-review

19 Scopus citations

Abstract

Topological entropy is one of the most difficult entropies to be used to analyze the DNA sequences, due to the finite sample and high-dimensionality problems. In order to overcome these problems, a generalized topological entropy is introduced. The relationship between the topological entropy and the generalized topological entropy is compared, which shows the topological entropy is a special case of the generalized entropy. As an application the generalized topological entropy in introns, exons and promoter regions was computed, respectively. The results indicate that the entropy of introns is higher than that of exons, and the entropy of the exons is higher than that of the promoter regions for each chromosome, which suggest that DNA sequence of the promoter regions is more regular than the exons and introns.

Original language	English
Article number	e88519
Journal	PLoS ONE
Volume	9
Issue number	2
DOIs	https://doi.org/10.1371/journal.pone.0088519
State	Published - 12 Feb 2014
Externally published	Yes

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abstract = "Topological entropy is one of the most difficult entropies to be used to analyze the DNA sequences, due to the finite sample and high-dimensionality problems. In order to overcome these problems, a generalized topological entropy is introduced. The relationship between the topological entropy and the generalized topological entropy is compared, which shows the topological entropy is a special case of the generalized entropy. As an application the generalized topological entropy in introns, exons and promoter regions was computed, respectively. The results indicate that the entropy of introns is higher than that of exons, and the entropy of the exons is higher than that of the promoter regions for each chromosome, which suggest that DNA sequence of the promoter regions is more regular than the exons and introns.",

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AU - Jin, Shuilin

AU - Tan, Renjie

AU - Jiang, Qinghua

AU - Xu, Li

AU - Peng, Jiajie

AU - Wang, Yong

AU - Wang, Yadong

PY - 2014/2/12

Y1 - 2014/2/12

N2 - Topological entropy is one of the most difficult entropies to be used to analyze the DNA sequences, due to the finite sample and high-dimensionality problems. In order to overcome these problems, a generalized topological entropy is introduced. The relationship between the topological entropy and the generalized topological entropy is compared, which shows the topological entropy is a special case of the generalized entropy. As an application the generalized topological entropy in introns, exons and promoter regions was computed, respectively. The results indicate that the entropy of introns is higher than that of exons, and the entropy of the exons is higher than that of the promoter regions for each chromosome, which suggest that DNA sequence of the promoter regions is more regular than the exons and introns.

AB - Topological entropy is one of the most difficult entropies to be used to analyze the DNA sequences, due to the finite sample and high-dimensionality problems. In order to overcome these problems, a generalized topological entropy is introduced. The relationship between the topological entropy and the generalized topological entropy is compared, which shows the topological entropy is a special case of the generalized entropy. As an application the generalized topological entropy in introns, exons and promoter regions was computed, respectively. The results indicate that the entropy of introns is higher than that of exons, and the entropy of the exons is higher than that of the promoter regions for each chromosome, which suggest that DNA sequence of the promoter regions is more regular than the exons and introns.

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A generalized topological entropy for analyzing the complexity of DNA sequences

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