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

Zribi, Soumaya; Messaoudi, Imen; Lachiri, Zied

doi:10.1109/cadiag.2017.8075677

Cited by 1 publication

(1 citation statement)

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“…To achieve this conversion operation, different coding techniques have been proposed. The choice of the coding technique is delicate since that each method must be tested to see if it can enhance particular useful information [39]. These techniques can be defined by the substitution of nucleotides by numerical values according to the user's choice.…”

Section: Dna Coding Techniquesmentioning

confidence: 99%

Microsatellite’s Detection using the S -Transform Analysis based on the Synthetic and Experimental Coding

Zribi¹,

Messaoudi²,

Oueslati³

et al. 2019

ijacsa

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Microsatellite in genomic DNA sequence, or Short tandem repeat (STR). It is a class of tandem repeat that have repeated pattern with size of 2-6 base-pairs adjacent to each other. The detection of the specific tandem repeat is an important part of genetic diseases identification and it is also used in DNA fingerprinting and in evolutionary studies. Many tools based on string matching have been developed to detect microsatellites. However, these tools are based on prior information about repetitions in the sequence which cannot be always obtainable. For this, the signal processing techniques were suggested to overcome the limitations of the bioinformatic tools. In this paper, we use a new variant of the S-Transform which we apply to short tandem repeats signals. These signals are firstly obtained by applying different coding techniques to the DNA sequences. To further study the performance of the proposed method, we establish a comparison with different bioinformatics approaches (TRF, Mreps, Etandem) and three other methods of signal processing: The Adaptive S-Transform (AST), the Empirical Mode and Wavelet Decomposition (EMWD) and the Parametric Spectral Estimation (PSE) considering the AR model. This study indicates that our approach outperforms the earlier methods in identifying the short tandem repeat, in fact, our method detects the exact number and positions of trinucleotides present in the tested real DNA sequence.

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Section: Dna Coding Techniquesmentioning

confidence: 99%