CSDL Home IEEE/ACM Transactions on Computational Biology and Bioinformatics 2014 vol.11 Issue No.05 - Sept.-Oct.
Building Specific Signals from Frequency Chaos Game and Revealing Periodicities Using a Smoothed Fourier Analysis
Issue No.05 - Sept.-Oct. (2014 vol.11)
Imen Messaoudi , Electrical Engineering Department, National Engineering School of Tunis, Tunisia
Afef Elloumi-Oueslati , Electrical Engineering Department, National Engineering School of Tunis, Tunisia
Zied Lachiri , Physics and Instrumentation Department, National Institute of Applied Sciences and Technology, Tunisia
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.
Chaos, DNA, Games, Genomics, Bioinformatics, Encoding, IEEE transactions,smoothed Fourier transform, Binary indicators, frequency chaos game signals, periodicities, signature
Imen Messaoudi, Afef Elloumi-Oueslati, Zied Lachiri, "Building Specific Signals from Frequency Chaos Game and Revealing Periodicities Using a Smoothed Fourier Analysis", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.11, no. 5, pp. 863-877, Sept.-Oct. 2014, doi:10.1109/TCBB.2014.2315991