Predicting Nucleosome Positions in Yeast: Using the Absolute Frequency

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.

Key words: Nucleosome position; Nucleosome DNA; Linker DNA; 2-mer absolute frequency.

This article can be cited as:
Z. Zhang, Y. Zhang, I. Gutman , Predicting Nucleosome Positions in Yeast: Using the Absolute Frequency J. Biomol Struct Dyn 29(5), 1081-1088 (2012).

Zhiqian Zhang1
Yusen Zhang1*
Ivan Gutman2

1School of Mathematics and Statistics, Shandong University at Weihai, Weihai 264209, China
2Faculty of Science, University of Kragujevac, P. O. Box 60, 34000 Kragujevac, Serbia

*Corresponding author: Zhiqian Zhang *E-mail: zhangys@sdu.edu.cn

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