Title: Detecting particular features in C. elegans genomes using Synchronous Analysis based on Wavelet Transform

Authors: Afef Elloumi Oueslati, Zied Lachiri, Noureddine Ellouze

Addresses: Unite Signal, Image et Reconnaissance de Formes, Departement de Genie Electrique, ENIT, BP 37, Campus Universitaire, Le Belvedere, 1002, Tunis, Tunisie. ' Departement de Genie Physique et Instrumentation, INSAT, BP 676, Centre Urbain Cedex, 1080, Tunis, Tunisie. ' Unite Signal, Image et Reconnaissance de Formes, Departement de Genie Electrique, ENIT, BP 37, Campus Universitaire, Le Belvedere, 1002, Tunis, Tunisie

Abstract: In this paper, synchronous analysis based on wavelet transform is applied to genomic sequences. To focus on the particular feature of periodicity 3 in the protein-coding region of genes, a coding method is applied on the sequence, which will be segmented to form a pitch synchronous representation. This modelling concept captures period of period fluctuation of signals. The wavelet transform enhances the periodicity, and a given threshold is used to make decision about exon|s positions. The algorithm simulation shows the accuracy of the method in simultaneously locating exons and revealing the reading frame associated.

Keywords: pitch synchronous representation; pitch synchronous wavelet transform; periodicity 3; C. elegans genome; protein coding regions; reading frame; bioinformatics; genomic sequences.

DOI: 10.1504/IJBRA.2011.040096

International Journal of Bioinformatics Research and Applications, 2011 Vol.7 No.2, pp.183 - 201

Accepted: 29 Oct 2010
Published online: 13 May 2011 *

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