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Title

 

 

 

 

 

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

 

Authors

 

Qinqin Wu1,2,*, Jiajun Wang2 and Hong Yan1,3

 

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

 

Email

 

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 Publishing Group

 

Copyright

Publisher

 

Copyright Transfer Agreement

 

The authors of published articles in Bioinformation automatically transfer the copyright to the publisher upon formal acceptance. However, the authors reserve right to use the information contained in the article for non commercial purposes.

 

License

 

 

This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.