A Study of the Potential of EIIP Mapping Method in Exon Prediction Using the Frequency Domain Techniques

Abstract

Recently, a number of numerical DNA sequence representations have evolved in order to transform the DNA sequence analysis problems from the traditional string processing domain to the discrete signal processing domain. On the other hand, the coding regions (exons) detection problem has received a special attention due to the 3-base periodicity property of exons which can be easily detected using simple discrete signal processing techniques. The 3-base periodicity in the nucleotide arrangement is evidenced as a sharp peak at frequency f =1/3 in the frequency domain power spectrum. In this paper, we exploit the 3-base periodicity property of a set of the Electron-Ion Interaction Pseudopotential (EIIP) coded DNA sequences by employing a frequency domain power spectrum estimation techniques as Short Time Fourier Transform (STFT),Auto Regressive (AR), Singular Vector Decomposition (SVD) and Digital filtering methods. Also, we give a brief comparison of these methods In order to enhance the coding prediction performance as well as the computa- tional complexity. Results provided that both STFT and digital filtering techniques for EIIP coded sequences performs with highest accuracy compared with AR and SVD methods.