Detection of Tandem Repeats in DNA Sequences Based on Parametric Spectral Estimation

Author

Zhou, Hongxia ; Du, Liping ; Yan, Hong

Author_Institution

Dept. of Electron. Eng., City Univ. of Hong Kong, Kowloon, China

Volume

13

Issue

5

fYear

2009

Firstpage

747

Lastpage

755

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.

Keywords

DNA; autoregressive processes; genomics; parameter estimation; DNA sequences; autoregressive model; diseases; gene regulatory function; genomes; parametric spectral estimation; tandem repeats detection; Autoregressive (AR) model; Autoregressive model; DNA sequence analysis; Spectral analysis; Tandem repeats; spectral analysis; tandem repeats; Algorithms; Base Sequence; Molecular Sequence Data; Sequence Analysis, DNA; Signal Processing, Computer-Assisted; Tandem Repeat Sequences;

fLanguage

English

Journal_Title

Information Technology in Biomedicine, IEEE Transactions on

Publisher

ieee

ISSN

1089-7771

Type

jour

DOI

10.1109/TITB.2008.920626

Filename

4472917