Gene Prediction by the Scale-limited Gabor Wavelet Transform for Identifying the Protein Coding Regions

Abstract

The identification of protein coding regions is one of the important applications of genome sequence analysis. Many digital signal processing (DSP) based methods, which rely on 3-base periodicity of DNA sequences, have been proposed. However, for most Fourier Transform based methods, a prior time-domain window length limits their performances. Even though several wavelet-based methods get rid of the dependence of window length, an overly wide scale range results in the loss of identification accuracy of these methods. In this paper, we propose a novel method based on Scale-limited Gabor Wavelet Transform (SLGWT) for identifying protein coding regions. This method inherits the advantage of wavelet-based methods in the independence of time-domain window length, while maintaining the consistent performance under different wavelet window lengths. More importantly, compared with other wavelet-based method, SLGWT identifies coding regions under narrower and more suitable scale range, thereby improving the identification accuracy and reducing computational load. The experimentations in the sequence and dataset levels verify the superiority of our proposed method.