An Adaptive Mapping Method Using Spectral Envelope Approach for DNA Spectral Analysis

Abstract

The digital signal processing approaches were investigated as a preliminary indicator for discriminating between the protein coding and non-coding regions of DNA. This is because a three-base periodicity (TBP) has already been proven to exist in protein-coding regions arising from the length of codons (three nucleic acids). This demonstrates that there is a prominent peak in the energy spectrum of a DNA coding sequence at frequency 13 rad/sample. However, because DNA sequences are symbolic sequences, these should be mapped into one or more signals such that the hidden information is highlighted. We propose, therefore, two new algorithms for computing adaptive mappings and, by using them, finding periodicities. Both such algorithms are based on the spectral envelope approach. This adaptive approach is essentially important since a single mapping for any DNA sequence may ignore its intrinsic properties. Finally, the improved performance of the new methods is verified by using them with synthetic and real DNA sequences as compared to the classical methods, especially the minimum entropy mapping (MEM) spectrum, which is also an adaptive method. We demonstrated that our method is both more accurate and more responsive than all its counterparts. This is especially important in this application since it reduces the risks of a coding sequence being missed.

Keywords

• DNA periodicities
• genomic signal processing
• spectral envelope
• spectral analysis
• symbolic sequence
• three-base periodicity