Imen Messaoudi

Building specific signals from frequency chaos game and revealing periodicities using a smoothed Fourier analysis

Investigating the roles and functions of DNA within genomes is becoming a primary focus of genomic research. Thus, the research works are moving towards cooperation between different scientific disciplines which aims at facilitating the interpretation of genetic information. In order to characterize the DNA of living organisms, signal processing tools appear to be very suitable for such study. However, a DNA sequence must be converted into a numerical sequence before processing; which defines the concept of DNA coding. In line with this, we propose a new one dimensional model based on the chaos game representation theory called Frequency Chaos Game Signal: FCGS. Then, we perform a Smoothed Fourier Transform to enhance hidden periodicities in the C.elegans DNA sequences. Through this study, we demonstrate the performance of our coding approach in highlighting characteristic periodicities. Indeed, several periodicities are shown to be involved in the 1D spectra and the 2D spectrograms of FCGSs. To investigate further about the contribution of our method in the enhancement of characteristic spectral attributes, a comparison with a range of binary indicators is established.

Spectral Analysis of Global Behaviour of C. Elegans Chromosomes

Afef Elloumi Oueslati1, Imen Messaoudi1, Zied Lachiri2 and Noureddine Ellouze1 Unite Signal, Image et Reconnaissance de Formes, Departement de Genie Electrique, 1Ecole Nationale d’Ingenieurs de Tunis, BP 37, Campus Universitaire, Le Belvedere, 1002, Tunis, 2Departement de Genie Physique et Instrumentation Institut National des Sciences Appliquees et de Technologie, BP 676, Centre Urbain Cedex, 1080, Tunis, Tunisie

Wavelet analysis of frequency chaos game signal: a time-frequency signature of the C. elegans DNA

Challenging tasks are encountered in the field of bioinformatics. The choice of the genomic sequence’s mapping technique is one the most fastidious tasks. It shows that a judicious choice would serve in examining periodic patterns distribution that concord with the underlying structure of genomes. Despite that, searching for a coding technique that can highlight all the information contained in the DNA has not yet attracted the attention it deserves. In this paper, we propose a new mapping technique based on the chaos game theory that we call the frequency chaos game signal (FCGS). The particularity of the FCGS coding resides in exploiting the statistical properties of the genomic sequence itself. This may reflect important structural and organizational features of DNA. To prove the usefulness of the FCGS approach in the detection of different local periodic patterns, we use the wavelet analysis because it provides access to information that can be obscured by other time-frequency methods such as the Fourier analysis. Thus, we apply the continuous wavelet transform (CWT) with the complex Morlet wavelet as a mother wavelet function. Scalograms that relate to the organism Caenorhabditis elegans (C. elegans) exhibit a multitude of periodic organization of specific DNA sequences.

Genomic data visualization

The sequencing of DNA implies an exponentially growing number of genomic data. This mass of information requires excessive work to reveal the location and functions of the characteristic areas in the genomes. In order to make exploratory studies, the alphabets of a DNA sequence need to be mapped onto their corresponding numerical values for visualization and analysis. This paper develops and compares a number of one dimensional and two dimensional mapping approaches. These coding techniques involve the alignment of bases in the polypeptide chains or affect the 3D structure of the DNA molecule.

Classification of Helitron’s Types in the C.elegans Genome based on Features Extracted from Wavelet Transform and SVM Methods

Helitrons, a sub-class of the Transposable elements class 2, are considered as an important DNA type. In fact, they contribute in mechanism’s evolution. Till now, these elements are not well studied using the automatic tools. In fact, the researches done in helitrons recognition are based only on biological experiments. In this paper, we propose an automatic method for characterizing helitrons by global signature and classifying the helitron’s types in C.elegans genome. For this goal, we used the Complex Morlet Wavelet Transform to generate helitron’s signatures (helitron’s scalograms presentation) and to extract the features of each category. Then, we used the SVM-classifier to classify these 10 helitron’s families. After testing different kernels and using the cross validation function, we present the best classification results given by the RBF-kernel with c=60, σ=0. 0000000015625 and OAO approach.

Helitron’s Periodicities Identification in C.Elegans based on the Smoothed Spectral Analysis and the Frequency Chaos Game Signal Coding

Helitrons are typical rolling circle transposons which make up the bulk of eukaryotic genomes. Unlike of other DNA transposons, these transposable elements (TEs), don’t create target site duplications or end in inverted repeats, which make them particular challenge to identify and more difficult to annotate. To date, these elements are not well studied; they only attracted the interest of researchers in biology. The focus of this paper is oriented towards identifying the helitrons in C.elegans genome in the perspective of signal processing. Aiming at the helitrons identification, a novel methodology including two steps is proposed: the coding and the spectral analysis. The first step consists in converting DNA into a 1-D signal based on the statistical features of the sequence (FCGS coding). As for the second step, it aims to identify the global periodicities in helitrons using the Smoothed Fourier Transform. The resulting spectrum and spectrogram are shown to present a specific signature of each helitron’s type.

A combined support vector machine-FCGS classification based on the wavelet transform for Helitrons recognition in C.elegans

The Helitrons, an important sub-class of the transposable elements (TEs) class II, have been revealed in diverse eukaryotic genomes. They are mobile elements with great impact on genomic evolution. Till today, there is no systematic classification model of helitrons; that’s why we thought of creating an efficient automatic model to identify these sequences. This paper focuses on the discrimination between helitrons and non-helitrons using the Support Vector Machine (SVM). In this study, we use all the SVM kernels and the higher accuracy rates are obtained by reaching the optimal kernels-parameters (d, c and σ). Further, we introduce two methods to represent the genomic sequences in the form of features to be considered later for the classification task: (i) the temporal and the spectral features extracted from the Frequency Chaos Game Signals order 2 (FCGS2) (ii) the features extracted from the Continuous Wavelet Transform (CWT) applied to the FCGS2 signals. The dataset we used regards two types DNA classes in C.elegans: the helitrons and the repetitive DNA sequences that contain microsatellites and do not form helitrons. The classification results prove that the wavelet energy feature is more effective than the FCGS2 features in the helitron’s recognition system. The performance of our system achieves a high recognition rate (Globally accuracy rate) reaching the value of 92.27%.

Tandem repeats detection based on S-transform applied on synthetic and experimental codings

In eukaryotic genomes, at least two adjacent duplicates of pattern nucleotides are considered as a tandem repeat. They are the major causes of several genetic diseases. Consequently, locating and characterizing them is of a crucial importance. Bioinformatics tools still very unsatisfactory in this domain, to use them, we need to have a preliminary knowledge about repetition which cannot always be available. Signal and image processing researchers turned towards different directions and looked up for more efficient methods to overcome bioinformatics tools inconvenience. In this paper we proceeded by using the S-Transform and tried several codings to sort the most convenient one for tandem repeats detection.

A Novel methodology for Helitron's classification by SVM based on time frequency representation

Helitron is considered as very important type of DNA involved in mechanisms evolution. These elements are not well studied and the major researches done are biological experiments. In this paper, we propose a novel approach aiming to characterize and classify helitrons types. Accordingly, we use the Support Vector Machine (SVM) classification technique known to be preferment in DNA related studies. We opt for the RBF kernel function after testing different kernel. Furthermore, we used the Wavelet coefficients features. These features are the direct result of the Complex Morlet Wavelet Transform applied to binary input form of DNA sequence resulting from the new FCGS coding technique.

Identification of microsatellites in DNA sequence based on S-transform

Microsatellites, or short tandem repeats (STRs), belong to the category of DNA tandem repeats which are present in all genomes with a size of 1 to 6 base-pairs. They are useful in several research domains such as population studies and DNA fingerprinting. They are also the cause of diverse genetic diseases. Thus, its important to characterize and define them. Bioinformatics tools still deficient in this field because they demand a prior knowledge of repeat. Things which cannot be always available in databases. Signal and image processing scientists looked up for more efficient methods to remediate to these tools limits. In this paper, we investigate microsatellites’ characterization in the DNA sequence using a new modification on the S-Transform (ST) analysis applied on the PNUC coding. To study further about the contribution of our method in the detection of STRs, a comparison with different methods including bioinformatics tools (TRF, Mreps, Etandem, AST, PSE, EMWD and Parametric) is established.