**8. Acknowlegements**

The author thanks Valerie Christian McDougall for her work on improving the presentation of this manuscript.

The source code that implements GOSH-FFT is available in a software package named VisioLab from the following website: http://www.ict.griffith.edu.au/sheridan/

## **9. References**


20 Will-be-set-by-IN-TECH

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**8** 

**Spectral Analysis of Global** 

Afef Elloumi Oueslati1, Imen Messaoudi1, Zied Lachiri2 and Noureddine Ellouze1

*2Département de Génie Physique et Instrumentation* 

*Le Belvédère, 1002, Tunis,* 

*Tunisie* 

*Centre Urbain Cedex, 1080, Tunis,* 

**Behaviour of C. Elegans Chromosomes** 

*1Ecole Nationale d'Ingénieurs de Tunis, BP 37, Campus Universitaire,* 

*Institut National des Sciences Appliquées et de Technologie, BP 676,* 

*Unité Signal, Image et Reconnaissance de Formes, Département de Génie Electrique,* 

Fourier analysis is one of the most useful decomposition into frequency bands to provide a signal's variations and irregularities measure. DNA spectral analysis based on Fourier Transform contributes in the systematic search of special DNA patterns which may correspond to biological important markers. For example, the Fourier harmonic analysis of the occurrence of a base "A" can give us the corresponding frequency with amplitude and a phase without being able to locate it in time. However it is interesting to also detect the moments of "silence" of base "A" i.e. the moments when this base does not exist. Such a representation of Fourier is thus limited with signals which contain transitory elements or evolutions in their spectral contents. For these non stationary signals, the DNA sequences, to highlight the frequency behavior, it becomes necessary to give the frequency the possibility of changes over time. It's the time frequency analysis aim assured by the Short Time Fourier Transform. In fact, the punctual aspect is very important to localize particular regions in chromosomes, to characterize the beginning of a protein coding regions or a nucleosome or its end. By depicting the frequencies by a smoothed STFT, a 2D or 3D spectrogram representation, specific regions appear distinctly. In this paper, we are concerned with the periodicities 3, 6, 9 and 10.5. The periodicity 3 discussed in (Anastassiou, 2001; Berger et al, 2003; Cohanim et al, 2005; Kornberg, 1977; Segal et al, 2006; Susillo et al 2003; Trifonov & Sussman, 1980; Trifonov, 1998; Vaidyanathan & Yoon, 2004) is related with protein coding regions (called exons) in the gene. The periodicity 10.5 is related with nucleosome's positions in the DNA sequence and the degree of deformability of the sequence in the DNA helix (Hayes et al, 1990; Trifonov & Sussman, 1980; Widom, 1996; Worcel et al 1981). The

This chapter is divided in five parts. First, we expose an introduction for relevant regions on chromosomes. In part three, we detailed the DNA's sequence analysis approach, related to sequence global behavior problem. It exposes the spectral analysis, which follows a certain

periodicity 6 and 9 are specific to C. Elegans organism.

**1. Introduction** 

