Gene and Exon Prediction Using Allpass-based Filters

It is well-known that the protein-coding regions of DNA sequences exhibit a period-3 behavior due to codon structure. These regions are often identified with the help of techniques such as the windowed DFT. It has been demonstrated in the past that identification of the period-3 regions helps in predicting the gene locations, and in fact allows the prediction of specific exons within the genes of eucaryotic cells. In this paper we introduce a simple and efficient scheme for identifying the period-3 regions of DNA sequences based on antinotch IIR filters instead of the DFT. These filters can be implemented very efficiently using the one-multiplier Gray and Markel lattice structure.