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

Abstract

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 500bp. 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.

A new way to visualize DNA’s base succession: the Caenorhabditis elegans chromosome landscapes

“…Three signal processing techniques, dealing with frequency band decomposition, are generally used: the frequency technique, the time-frequency technique and the time scale technique. The first one, which is based on Fourier transform, contributes in the systematic search of DNA periodicities which may correspond to biological important markers for the global behavior [15,33,36,45]. The Fourier harmonic analysis of the occurrence of base groups can give us the corresponding frequency with amplitude and a phase.…”

“…For these non-stationary signals, particularly the DNA sequences, to highlight the frequency behavior, it becomes necessary to give the frequency the possibility of changes over time. It is the time-frequency analysis aim, and it is assured by the short-time Fourier transform (STFT) [6,36,43]. The punctual aspect is very important to localize particular regions in chromosomes, to characterize the beginning of a protein coding regions or a nucleosomes or its end [33,36].…”

“…It is the time-frequency analysis aim, and it is assured by the short-time Fourier transform (STFT) [6,36,43]. The punctual aspect is very important to localize particular regions in chromosomes, to characterize the beginning of a protein coding regions or a nucleosomes or its end [33,36]. By depicting the frequencies by a smoothed STFT, a 2D or 3D spectrogram representation [6,34,43] of specific regions can appear but without details because of the uncertainty principle of Heisenberg "the more precisely the position is determined, the less precisely the momentum is known in this instant, and vice versa" [21].…”

A Coding Technique Based on the Frequency Evolution Creates with a Time Frequency Analysis a New Genome's Landscape

“…The latter frequency is generally related to the nucleosome formation [10] [11] [36][37][38][39]. However, in the subfigure (c), energy level decreases.…”

“…Within the context of the genomic signal processing, the joint time-frequency analysis based on the Fourier transform has played a key role in the data characterization and visualization [8][9][10][11]. In fact, the color spectrograms were shown to provide significant information about periodicities and recurrent motifs along the bio-molecular sequences [8] [9].…”