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Bioinformatics Advance Access published online on January 31, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm008
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

OMWSA: detection of DNA repeats using moving window spectral analysis

Liping Du 1, Hongxia Zhou 1 and Hong Yan 1,2,*

1Department of Electronic Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong,
2School of Electrical and Information Engineering, University of Sydney, NSW2006, Sydney, Australia.

*To whom correspondence should be addressed. Hong Yan, E-mail: h.yan{at}cityu.edu.hk


  Abstract

Summary: Repetitive DNA sequences play paramount biological roles, such as gene variation and regulatory functions on gene expressions. Until now, detection of various kinds of DNA repeats accurately is still an open problem. In this paper, we propose a new method and a visualization tool for detecting DNA repeats in a 2D plane of location and frequency by using optimized moving window spectral analysis. The spectrogram can display the general distribution of repetitive sequences while showing the repeat period, length and location without any prior knowledge. Experiment results demonstrate that our method is accurate and robust even under the condition of excessive mutating and interleaving.

Availability: Software is available upon request

Associate Editor: Golan Yona

Received on July 28, 2006; revised on December 3, 2006; accepted on January 14, 2007

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