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Identification of Protein Coding Region of DNA Sequence Using Multirate Filter

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Computational Advancement in Communication Circuits and Systems

Part of the book series: Lecture Notes in Electrical Engineering ((LNEE,volume 335))

Abstract

Gene predication is an important part of genomic signal processing (GSP) to identify the protein coding region of a DNA sequence. Discrete Fourier Transform (DFT) technique is most popular method for period-3 peaks identification for long time which generates various harmonics; generally known as 1/f noise along with sharp peaks, which may lead to false predication of coding region. Previous researchers used different types of filter to suppress this noise. The author in this article used a multirate filter along with anti-notch filter to suppress the noise and performance of the filter is measured by signal-to-noise ratio (SNR).

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References

  1. D. Anastassiou, Frequency—domain analysis of biomolecular sequences. Bioinformatics 16, 1073–1081 (2000)

    Article  MathSciNet  Google Scholar 

  2. D. Anastassiou, DSP in genomics: processing and frequency domain analysis of character strings. IEEE-7803-7041-2001 (2001)

    Google Scholar 

  3. S Tiwari, S. Ramachandran, A. Bhattacharya, S. Bhattacharya, R. Ramaswamy, Prediction of probable genes by fourier analysis of genomic sequences. CABIOS 3(3), 263–270 (1997)

    Google Scholar 

  4. C. Yin, S. Stephen, T. Yau, Prediction of protein coding regions by the 3 base periodicity analysis of a DNA sequence. J. Theoret. Biol. 247, 687–694 (2007)

    Article  MathSciNet  Google Scholar 

  5. E.N. Trifonov, J.L. Sussman, The pitch of chromatin DNA is reflected in its nucleotide sequence. Proc. Natl. Acad. Sci. USA 77, 3816–3820 (1980)

    Article  Google Scholar 

  6. P.P. Vaidyanathan, B.J. Yoon, The role of signal-processing concepts in genomics and proteomics. J. Franklin Inst. (Special Issue on Genomics) (2004)

    Google Scholar 

  7. J. Tuqan, A. Rushdi, A DSP perspective to the period—3 detection problem, in Proceedings of the IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS (2006), pp. 53–54

    Google Scholar 

  8. J. Epps, E. Ambikairajah, M. Akhtar, An integer period DFT for biological sequence processing, in Proceedings of the IEEE International Workshop on Genomic Signal Processing and Statistics GENSIPS (2008), pp. 1–4

    Google Scholar 

  9. R. Kakumani, V. Devabhaktuni, Prediction of protein coding regions in DNA sequence using a model based approach, in IEEE Explore (2008) pp. 1918–1920. ISBN:978-1-4244-1684-4/08

    Google Scholar 

  10. M. Roy, S. Biswas, S. Barman(Mandal), Identification and analysis of coding and non-coding regions of a DNA sequence by positional frequency distribution of nucleotides (PFDN) algorithm, in International Conference on Computers and Devices for Communication (CODEC) (2009)

    Google Scholar 

  11. S. Barman(Mandal), S. Biswas, S. Das, M. Roy, Performance analysis and simulation of IIR anti-notch filter with various structures for gene predication application, in 5th International Conference on Computer and Devices for Communication (CODEC) (2012)

    Google Scholar 

  12. R.F. Voss, Evolution of long-range fractal correlation and 1/f noise in DNA base sequences. Phys. Rev. Lett. 68(25), 3805–3808 (1992)

    Article  Google Scholar 

  13. National Centre for Biotechnology Information (NCBI). http://www.ncbi.nlm.nih.gov

  14. M. Vetterli, A theory of multirate filter banks. IEEE Trans. Acoust. Speech Signal Process. 35(3), 356–372 (1987)

    Google Scholar 

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Correspondence to S. Singha Roy .

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Singha Roy, S., Barman, S. (2015). Identification of Protein Coding Region of DNA Sequence Using Multirate Filter. In: Maharatna, K., Dalapati, G., Banerjee, P., Mallick, A., Mukherjee, M. (eds) Computational Advancement in Communication Circuits and Systems. Lecture Notes in Electrical Engineering, vol 335. Springer, New Delhi. https://doi.org/10.1007/978-81-322-2274-3_16

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  • DOI: https://doi.org/10.1007/978-81-322-2274-3_16

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  • Publisher Name: Springer, New Delhi

  • Print ISBN: 978-81-322-2273-6

  • Online ISBN: 978-81-322-2274-3

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