Open Access

Short Exon Detection in DNA Sequences Based on Multifeature Spectral Analysis

EURASIP Journal on Advances in Signal Processing20102011:780794

https://doi.org/10.1155/2011/780794

Received: 30 June 2010

Accepted: 31 October 2010

Published: 2 November 2010

Abstract

This paper presents a new technique for the detection of short exons in DNA sequences. In this method, we analyze four DNA structural properties, which include the DNA bending stiffness, disrupt energy, free energy, and propeller twist, using the autoregressive (AR) model. The linear prediction matrices for the four features are combined to find the same set of linear prediction coefficients, from which we estimate the spectrum of the DNA sequence and detect exons based on the 1/3 frequency component. To overcome the nonstationarity of DNA sequences, we use moving windows of different sizes in the AR model. Experiments on the human genome show that our multi-feature based method is superior in performance to existing exon detection algorithms.

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Authors’ Affiliations

(1)
Department of Electronic Engineering, City University of Hong Kong

Copyright

© N. Y. Song and H. Yan. 2011

This article is published under license to BioMed Central Ltd. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.