Title: DSP techniques for protein coding region identification based on background noise and nonlinear phase delay reduction from period-3 spectrum using zero phased anti-notch filter and Savitzky-Golay (S-G) filter
Authors: Amit Kumar Singh; Vinay Kumar Srivastava
Addresses: Electronics and Communication Engineering Department, Motilal Nehru National Institute of Technology, Pryagraj, Allahabad, Uttar Pradesh, 211004, India ' Electronics and Communication Engineering Department, Motilal Nehru National Institute of Technology, Pryagraj, Allahabad, Uttar Pradesh, 211004, India
Abstract: Short time discrete Fourier transform (STDFT) and anti-notch filters (ANF) are perhaps the most common DSP tools that uses the period-3 feature of protein coding sequences to discriminate between protein-coding regions and noncoding regions. However, the performance of these techniques is still limited due to the background noise present in their period-3 spectrum. The drawback with existing de-noising techniques is that it also distorts the period-3 feature besides noise suppression. In this article, the Savitzky-Golay (SG) filter is used to suppress the background noise from period-3 spectrum. A zero phased anti-notch filter (ZANF) is also used to overcome the effect of nonlinear phase delay from the period-3 spectrum of ANF. It is obtained that the combined use of ZANF and SG filters increases the prediction accuracy of conventional ANF by around 19% -26%.
Keywords: protein coding region prediction; 3-base periodicity; short time discrete Fourier transform; moving average filter; Savitzky-Golay (S-G) filter.
International Journal of Computational Biology and Drug Design, 2021 Vol.14 No.5, pp.343 - 363
Received: 27 May 2020
Accepted: 12 Jun 2021
Published online: 07 Jan 2022 *