文章基本信息

标题：Microsatellite’s Detection using the S -Transform Analysis based on the Synthetic and Experimental Coding
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作者：Soumaya Zribi ; Imen Messaoudi ; Afef Elloumi Oueslati 等
期刊名称：International Journal of Advanced Computer Science and Applications(IJACSA)
印刷版ISSN：2158-107X
电子版ISSN：2156-5570
出版年度：2019
卷号：10
期号：3
页码：254-263
DOI：10.14569/IJACSA.2019.0100333
出版社：Science and Information Society (SAI)
摘要：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.
关键词：DNA sequence; microsatellites; synthetic and experimental coding; s-transform; bioinformatic tools; Empirical Mode and Wavelet Decomposition (EMWD); Parametric Spectral Estimation (PSE)