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

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.

@article{Zribi2019,
  title     = {Microsatellite’s Detection using the S -Transform Analysis based on the Synthetic and Experimental Coding},
  journal   = {International Journal of Advanced Computer Science and Applications},
  volume    = {10},
  number    = {3},
  year      = {2019},
  publisher = {The Science and Information Organization},
  author    = {Soumaya Zribi and Imen Messaoudi and Afef Elloumi Oueslati and Zied Lachiri},
  doi       = {10.14569/IJACSA.2019.0100333},
  url       = {https://doi.org/10.14569/IJACSA.2019.0100333}
}