Article: Genome-wide nucleosome detection based on the dinucleotide position frequencies Journal: International Journal of Data Mining and Bioinformatics (IJDMB) 2014 Vol.10 No.3 pp.285 - 299 Abstract: It has been discovered that the properties of nucleosome-bound and linker DNA sequences have important effects on nucleosome positioning. On the other hand, the position frequencies of the nucleosome-bound and linker DNA reveal most of their statistical properties. Therefore, two methods based on the statistical properties of the DNA sequences are proposed for nucleosome positioning. The first method defines the score profile based on the position-frequency differences of some dinucleotides which are most different in the nucleosome-bound and linker DNAs. Our second method is defined by combining the differences in dinucleotide position frequencies and the periodicity of nucleosome-bound DNAs. Experiment results on Saccharomyces cerevisiae show that our second method outperforms significantly other algorithms in nucleosome positioning performed in our paper. Furthermore, this algorithm also achieves the highest accuracy and F-score on the Simian virus 40 chromatin even if the dinucleotide position-frequency data are extracted from the S. cerevisiae. Inderscience Publishers - linking academia, business and industry through research

Title: Genome-wide nucleosome detection based on the dinucleotide position frequencies

Authors: Xing Huang; Jiajun Wang; Hong Yan

Addresses: School of Electronic and Information Engineering, Soochow University, Suzhou 215006, China ' School of Electronic and Information Engineering, Soochow University, Suzhou 215006, China ' Department of Electronic Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong; School of Electrical and Information Engineering, University of Sydney, NSW 2006, Australia

Abstract: It has been discovered that the properties of nucleosome-bound and linker DNA sequences have important effects on nucleosome positioning. On the other hand, the position frequencies of the nucleosome-bound and linker DNA reveal most of their statistical properties. Therefore, two methods based on the statistical properties of the DNA sequences are proposed for nucleosome positioning. The first method defines the score profile based on the position-frequency differences of some dinucleotides which are most different in the nucleosome-bound and linker DNAs. Our second method is defined by combining the differences in dinucleotide position frequencies and the periodicity of nucleosome-bound DNAs. Experiment results on Saccharomyces cerevisiae show that our second method outperforms significantly other algorithms in nucleosome positioning performed in our paper. Furthermore, this algorithm also achieves the highest accuracy and F-score on the Simian virus 40 chromatin even if the dinucleotide position-frequency data are extracted from the S. cerevisiae.

Keywords: nucleosome positioning; DNA sequences; dinucleotide position frequency; bioinformatics; nucleosome detection; Saccharomyces cerevisiae; S. cerevisiae.

DOI: 10.1504/IJDMB.2014.064531

International Journal of Data Mining and Bioinformatics, 2014 Vol.10 No.3, pp.285 - 299

Received: 10 May 2012
Accepted: 02 Aug 2012
Published online: 21 Oct 2014 *

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Title: Genome-wide nucleosome detection based on the dinucleotide position frequencies

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