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Building specific signals from Frequency Chaos Game and revealing periodicities using a Smoothed Fourier analysis
PrePrint
ISSN: 1545-5963
Investigating the roles and functions of DNA within genomes is becoming a primary focus of genomic research. Thus, the researches 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 comparaison with a range of binary indicators is established.
Index Terms:
Chaos,DNA,Games,Genomics,Bioinformatics,Encoding,IEEE transactions
Citation:
Afef 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, 21 April 2014. IEEE computer Society Digital Library. IEEE Computer Society, <http://doi.ieeecomputersociety.org/10.1109/TCBB.2014.2315991>
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