Detection of Coding Regions in Large DNA Sequences Using the Short Time Fourier Transform with Reduced Computational Load
Due to the non-uniform distribution of codons in coding regions, a three-periodicity is present in most of genome coding regions which, after a previous numeric conversion, show a notable peak at frequency component N/3 when calculating the Fourier Transform. Taking into account the veracity of this result, the Short Time Fourier Transform has been applied to large DNA sequences to predict coding regions. This paper presents a new approach to reduce the computational burden associated with STFT computation, for coding regions detection purposes. Experimental results show significant savings in computation time when the proposed algorithm is employed.
KeywordsFrequency Component Discrete Fourier Transform Computational Load Power Spectrum Analysis Short Time Fourier Transform
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- 3.Berger, J.A., Mitra, S.K., Astola, J.: Power spectrum analysis for DNA sequences. University of California (2002)Google Scholar
- 5.Berger, J.A., Mitra, S.K., Carli, M., Neri, A.: New approaches to genome sequence analysis based on digital signal processing. University of California (2002)Google Scholar
- 6.Su, S.-C., Yeh, C.H., Kuo, C.J.: Structural Analysis of Genomic Sequences with Matched Filtering. IEEE Signal Proccessing Magazine 3, 2893–2896 (2003)Google Scholar
- 7.Kotlar, D., Lavner, Y.: Gene Prediction by Spectral Rotation Measure: A New Method for Identifying Protein-Coding Regions. Genome Research 13, 1930–1937 (2003)Google Scholar
- 8.Berger, J.A., Mitra, S.K., Astola, J.: Power spectrum analysis for DNA sequences. In: Proceedings of the International Symposium on Signal Processing and its Applications (ISSPA 2003), Paris, France, pp. 29–32 (2003)Google Scholar