Signal processing in sequence analysis: Advances in eukaryotic gene prediction

Abstract

Genomic sequence processing has been an active area of research for the past two decades and has increasingly attracted the attention of digital signal processing researchers in recent years. A challenging open problem in deoxyribonucleic acid (DNA) sequence analysis is maximizing the prediction accuracy of eukaryotic gene locations and thereby protein coding regions. In this paper, DNA symbolic-to-numeric representations are presented and compared with existing techniques in terms of relative accuracy for the gene and exon prediction problem. Novel signal processing-based gene and exon prediction methods are then evaluated together with existing approaches at a nucleotide level using the Burset/ Guigo1996, HMR195, and GENSCAN standard genomic datasets. A new technique for the recognition of acceptor splice sites is then proposed, which combines signal processing-based gene and exon prediction methods with an existing data-driven statistical method. By comparison with the acceptor splice site detection method used in the gene-finding program GENSCAN, the proposed DSP-statistical hybrid technique reveals a consistent reduction in false positives at different levels of sensitivity, averaging a 43% reduction when evaluated on the GENSCAN test set. © 2008 IEEE.