Low Complexity Frequency Monitoring Filter for Fast Exon Prediction Sequence Analysis

Abstract

Over the last few years, the application of Digital Signal Processing (DSP) techniques for genomic sequence analysis has received great interest. Indeed, among its applications in genomic analysis, it has been demonstrated that DSP can be used to detect protein coding regions (exons) among non-coding regions in a DNA sequence. The period-3 behavior exhibited by exons is one of its features that has been exploited in several developed algorithms for exon prediction. Identification of this periodicity in genomic sequences can be done by using different methods such as the well-known Fast Fourier Transform (FFT) and the Goertzel algorithm for complexity reduction in which the reduction of computational time is a great challenge in genomic analysis. Therefore, this paper presents a novel one frequency analysis by using half of the arithmetic complexity of the Goertzel algorithm for gene prediction. Compared to the Intel®’s FFT (MKL) optimized function, the Goertzel’s (IPP) and the dedicated Goertzel compiled function with ICC on Xeon CPU (24 cores), the proposed method conserves the same accuracy provided by the referenced methods which will manifest a speedup of 3000, 10 and 2 compared to MKL FFT, IPP Goertzel and the dedicated Goertzel with ICC, respectively.