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

Authors:
Hongxia Zhou;Liping Du;Hong Yan
Affiliations:
Department of Electronic Engineering, City University of Hong Kong, Kowloon, Hong Kong;University of Science and Technology, Beijing, China and Department of Electronic Engineering, City University of Hong Kong, Kowloon, Hong Kong;Department of Electronic Engineering, City University of Hong Kong, Kowloon, Hong Kong and School of Electrical and Information Engineering, University of Sydney, NSW, Australia
Venue:
IEEE Transactions on Information Technology in Biomedicine - Special section on computational intelligence in medical systems
Year:
2009

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Abstract

Tandem repeats, which occur frequently in genomes, are related to gene regulatory functions and various diseases. In this paper, an efficient algorithm for tandem repeat detection is proposed. In our method, the spectrogram of a DNA sequence is analyzed based on the autoregressive model. Then, significant peaks in the spectrogram are selected, and the corresponding regions in the DNA sequence are analyzed to search for tandem repeats. Experiment results show that our method has a superior performance in comparison with other algorithms.