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

Abstract

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. Available on http://www.hy8.com/~tec/sw01/omwsa01.zip. Supplementary data are available at Bioinformatics online.