3D Spectrum Analysis of DNA Sequence: Application to Caenorhabditis elegans Genome

Abstract

A Fourier transform technique has been used to enhance the genome periodicities when analyzing the distributions of independent nucleotides and dinucleotides. These periodicities are varying from 2 to 500 bp. In this paper we focus on the 3 and 10.5 periodicities. The 3-base periodicity is characteristic for the protein-coding sequences only. The source of the approximately 10.5-base sequence period is related to the deformability of DNA. In fact, DNA folding in chromatin is facilitated by periodical positioning of some dinucleotides along the sequences, with the period close to 10.5 bases. When the DNA sequence is encoded for the signal 'AA' or 'TT' or 'TA' the peak at 10.5 is locally strengthened. For the Caenorhabditis elegans (C. Elegans) genome, this peak becomes the dominant feature in the transform. Studying one organism's genome requires three steps. First, the DNA coding method: the DNA's string data are transformed into numerical signal. Second, periodicities are detected by spectral analysis. Third, a 3D graphical representation allows following the evolution of this periodicity along the genome and facilitating the specific regions location.