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Denoising the 3-Base Periodicity Walks of DNA Sequences in Gene Finding

Changchuan Yin1, Dongchul Yoo2, and Stephen S.-T. Yau3
1. College of Natural Sciences, University of Phoenix Chicago Campus, IL 60173, USA
2. Department of Mathematics, Statistics and Computer Science, University of Illinois at Chicago
3. Department of Mathematical Sciences, Tsinghua University, Beijing
Abstract—A nonlinear Tracking-Differentiator is one-inputtwo-output system that can generate smooth approximation of measured signals and get the derivatives of the signals. The nonlinear tracking-Differentiator is explored to denoise and generate the derivatives of the walks of the 3-periodicity of DNA sequences. An improved algorithm for gene finding is presented using the nonlinear Tracking-Differentiator. The gene finding algorithm employs the 3-base periodicity of coding region. The 3-base periodicity DNA walks are denoised and tracked using the nonlinear Tracking- Differentiator. Case studies demonstrate that the nonlinear Tracking-Differentiator is an effective method to improve the accuracy of the gene finding algorithm.
 
Index Terms—genome, nonlinear tracking-differentiator, 3-periodicity, fourier transform

Cite: Changchuan Yin, Dongchul Yoo, and Stephen S.-T. Yau, "Denoising the 3-Base Periodicity Walks of DNA Sequences in Gene Finding", Journal of Medical and Bioengineering, vol. 2, no. 2, pp.80-83, 2013. doi: 10.12720/jomb.2.2.80-83
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