Prediction of nucleosome positions in the yeast genome based on matched mirror position filtering

Title

Prediction of nucleosome positions in the yeast genome based on matched mirror position filtering

Authors

Qinqin Wu^1,2,*, Jiajun Wang² and Hong Yan^1,3

Affiliation

¹Department of Electronic Engineering, City University of Hong Kong, Kowloon, Hong Kong; ²School of Electronics and Information Engineering, Soochow University, Suzhou, China; ³School of Electrical and Information Engineering, University of Sydney, NSW 2006, Australia

suzhouqinqin@gmail.com

Article Type

Hypothesis

Date

Received March 11, 2009; revised May 01, 2009; accepted June 22, 2009; published August 06, 2009

Abstract

Nucleosome positioning can affect the accessibility of the underlying DNA to the nuclear environment and as such plays an essential role in the regulation of cellular processes. Specific patterns have been found in the underlying DNA sequences of the nucleosome, and one of the most important patterns includes dinucleotides distributed every 10 to 11 base pairs. Based on this property, we propose to match each dinucleotide in the sequence against its mirror occurrences for 10 to 11 base pairs on both left-hand and right-hand sides. A large number of matches in a local region will then signify the existence of a nucleosome. In this paper, we propose the matched mirror position filters for efficient matching of periodic dinucleotide patterns and computationally predict the nucleosome positions. Experimental results on the Saccharomyces cerevisiae (yeast) genome show that the proposed algorithm can predict nucleosome positions effectively. More than 50% of our predicted nucleosomes are within 35 base pairs of those detected by biological experiments.

Keywords

mirror position filter; nucleosome positioning; Saccharomyces cerevisiae; yeast genome; DNA

Citation

Wu et al, Bioinformation 3(10): 454-459 (2009)

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.