Time and Frequency Domain Methods for Gene and Exon Prediction in Eukaryotes

The detection of period-3 components in exons of eukaryotic gene sequences enables signal processing based time-domain and frequency-domain methods to predict these regions. In this paper, we improve the prediction accuracy of frequency-domain methods by proposing a new algorithm known as the paired and weighted spectral rotation (PWSR) measure, which exploits both period-3 behaviour and another useful statistical property of genomic sequences. By comparison with existing frequency-domain approaches, the proposed PWSR method reveals relative improvements of 15.2% and 10.7% respectively over spectral content and spectral rotation measures in terms of prediction accuracy of exonic nucleotides at a 10% false positive rate using the GENSCAN test set. Finally, we combine the proposed PWSR with an existing time-domain method to demonstrate further signal processing-based improvements in gene and exon prediction accuracy.