Gene and exon prediction using time domain algorithms

Abstract

The protein-coding regions of DNA sequences normally exhibit a period-3 behaviour that can be used to identify gene locations. Various methods have been used to automatically identify the coding regions, however these have been predominantly ‘frequency’ domain techniques. Numerous ‘time’ domain techniques are available from the signal processing literature, and this work examines their applicability to gene and exon prediction in DNA sequences. Two techniques new to this application are introduced: the Time Domain Periodogram (TDP) and the Average Magnitude Difference Function (AMDF). We also present an indicative comparison of time domain and existing frequency domain techniques, from which the AMDF appears to be the most promising technique. Autoregressive modelling methods are further investigated in this work.