OMWSA: detection of DNA repeats using moving window spectral analysis

Authors:
Liping Du;Hongxia Zhou;Hong Yan
Affiliations:
Department of Electronic Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong;Department of Electronic Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong;Department of Electronic Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
Venue:
Bioinformatics
Year:
2007

Citing 0
Cited 2

Detection of tandem repeats in DNA sequences based on parametric spectral estimation

IEEE Transactions on Information Technology in Biomedicine - Special section on computational intelligence in medical systems
Detection and 2-Dimensional display of short tandem repeats based on signal decomposition

International Journal of Data Mining and Bioinformatics

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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 article, 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. Experimental results demonstrate that our method is accurate and robust even under the condition of excessive mutating and interleaving. Availability: Available on http://www.hy8.com/~tec/sw01/omwsa01.zip. Contact: h.yan@cityu.edu.hk Supplementary information: Supplementary data are available at Bioinformatics online.