Digital signal processing for gene prediction

Abstract

Identification of gene locations in a DNA sequence is one of the important problems in the area of genomics. Nucleotides in exons of a DNA sequence show f = 1/3 periodicity. The period-3 property in exons of eukaryotic gene sequences enables signal processing based time-domain and frequency-domain methods to predict these regions. Identification of the period-3 regions helps in predicting the gene locations within the billions long DNA sequence of eukaryotic cells. Existing non-parametric filtering techniques are less effective in detecting small exons. This paper presents a Harmonic Suppression filter and parametric Minimum Variance Spectrum estimation technique for gene prediction. We show that both the filtering techniques are able to detect smaller exon regions and adaptive MV filter minimizes the power in introns (non-coding regions) giving more suppression to the intron regions. Furthermore, 2-simplex mapping is used to reduce the computational complexity.