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Journal of Biomolecular Structure and Dynamics Volume 29, 2012 - Issue 5
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Original Articles

Predicting Nucleosome Positions in Yeast: Using the Absolute Frequency

Zhiqian Zhang School of Mathematics and Statistics, Shandong University at Weihai, Weihai, 264209, China
,
Yusen Zhang School of Mathematics and Statistics, Shandong University at Weihai, Weihai, 264209, China
&
Ivan Gutman Faculty of Science, University of Kragujevac, P. O. Box 60, 34000, Kragujevac, Serbia
Pages 1081-1088 | Received 08 Jul 2010, Published online: 11 Jul 2012
 
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Abstract

Nucleosome is the basic structure of chromatin in eukaryotic cells, and they form the chromatin fiber interconnected by sections of linker DNA. Nucleosome positioning is of great significance for gene transcription regulation. In this paper, we consider the difference of absolute frequency of nucleotides between the nucleosome forming and nucleosome inhibiting sequences. Based on the 2-mer absolute frequency of nucleotides in genome, a new model is constructed to distinguish nucleosome DNA and linker DNA. When used to predict DNA potential for forming nucleosomes in S. cerevisiae, the model achieved a high accuracy of 96.05%. Thus, the model is very useful for predicting nucleosome positioning.

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