A digital signal processing method for gene prediction with improved noise suppression

Authors:
Trevor W. Fox;Alex Carreira
Affiliations:
Research and Development Department, Intelligent Engines Corporation, Calgary, Alberta, Canada;Department of Electrical and Computer Engineering, University of Calgary, University Drive N.W., Calgary, Alberta, Canada
Venue:
EURASIP Journal on Applied Signal Processing
Year:
2004

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Abstract

It has been observed that the protein-coding regions of DNA sequences exhibit period-three behaviour, which can be exploited to predict the location of coding regions within genes. Previously, discrete Fourier transform (DFT) and digital filter-based methods have been used for the identification of coding regions. However, these methods do not significantly suppress the noncoding regions in the DNA spectrum at 2π/3. Consequently, a noncoding region may inadvertently be identified as a coding region. This paper introduces a new technique (a single digital filter operation followed by a quadratic window operation) that suppresses nearly all of the noncoding regions. The proposed method therefore improves the likelihood of correctly identifying coding regions in such genes.