Spectral techniques for classifying short exon and intron sequences

In the paper, the performances on FFT-based, FIR and IIR digital filter-based (DF-based) period-3 classifications of short exon and intron sequences of the human and eleven model organisms are studied. For each organism, sequences of 150-base length are chosen and 16,000 sequences are used for training and testing. FIR and IIR digital filter orders are chosen to be around a similar level of computational complexity as that of the FFT-based method. Also, three thresholds are considered. Simulation results indicate that the classification precisions obtained for different organisms are not the same probably due to their inherent genomic differences. Also, the FFT-based method, the FIR DF-based method (with filter order 24), and the IIR DF-based method (with filter order 6) can respectively yield top classifications in 9, 1, and 2 out of 12 organisms.