Identification of exon locations in DNA sequences using a fractional digital anti-notch filter

Abstract

Identification of protein coding region (exon) locations in DNA sequences is a fundamental initial step in genomic signal processing (GSP). Several techniques have already been applied to achieve this challenging task. However, improvements are still needed. Transforms-based methods and digital filtering are among those techniques that have been widely used. These techniques exploit the period-3 property of protein coding regions. This paper proposes the application of a narrowband bandpass fractional digital filter to extract more selectively the single frequency component corresponding to the frequency f=1/3 from DNA sequences. The ideal fractional digital anti-notch filter has an infinite amplitude at the central frequency and two tuning parameters which may be used to independently adjust the central frequency and the amplitude frequency response. The ideal filter has been approximated and implemented efficiently as an infinite impulse response (IIR) filter. The effectiveness of the proposed method has been assessed in terms of common performance evaluation metrics computed from the results obtained using DNA sequences taken from the National Center for Biotechnology Information (NCBI) and HMR195 datasets using different numerical transformations including Voss mapping and electron–ion potential (EIIP) representation. In addition to overcome the problem of sliding window size encountered in transform-based methods, comparison with existing state-of-the-art methods for exon location identification has demonstrated superiority of the proposed method on benchmark datasets.