OMWSA: detection of DNA repeats using moving window spectral analysis.
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.


BACKGROUND
Available on http://www.hy8.com/~tec/sw01/omwsa01.zip.


BACKGROUND
Supplementary data are available at Bioinformatics online.
Du
Liping
L
Department of Electronic Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong.
Zhou
Hongxia
H
Yan
Hong
H
D000465:Algorithms; D004247:DNA / Q000737:chemistry*; D005583:Fourier Analysis; D006801:Humans; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
D004247:DNA