Z-curve features are one of the popular features used in exon/intron classification. We showed that although both Z-curve and Fourier approaches are based on detecting 3-periodicity in coding regions, there are significant differences in their spectral formulation. From the spectral formulation of the Z-curve, we obtained three modified sequences that characterize different biological properties. Spectral analysis on the modified sequences showed a much more prominent 3-periodicity peak in coding regions than the Fourier approach. For long sequences, prominent peaks at 2Π/3 are observed at coding regions, whereas for short sequences, clearly discernible peaks are still visible. Better classification can be obtained using spectral features derived from the modified sequences.