Power spectrum analysis for DNA sequences

Certain biological functions are related to observe periodic behavior in DNA sequences, for example the period-3 behavior in exons. Appropriately, the field of digital signal processing has begun to contribute to the gene identification problem by allowing for discoveries in terms of these periodicities. This work presents known spectral analysis techniques that are applied in a new manner to find DNA sequences that exhibit periodic behavior in the residues. Improvements to the standard DFT power spectrum are shown by intuitively choosing new sequence alphabets. We also illustrate how power spectrums of the warped DFT and the Walsh-Hadamard transform provide useful frequency domain representations for finding such periodic behavior. Examples are given to illustrate the value of the competing techniques and to visually display comparisons.