Identification of protein coding regions using antinotch filters

  • Authors:

  • Malaya Kumar Hota;Vinay Kumar Srivastava

  • Affiliations:

  • Department of Electronics and Telecommunication Engineering, Synergy Institute of Engineering and Technology, Dhenkanal 759001, Odisha, India;Department of Electronics and Communication Engineering, Motilal Nehru National Institute of Technology, Allahabad 211004, Uttar Pradesh, India

  • Venue:
  • Digital Signal Processing
  • Year:
  • 2012

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Abstract

A major area of research in genomic sequence analysis is the identification of protein coding regions using the period-3 property. Previously antinotch filter has been used for this purpose. In this paper, three antinotch filters, namely conjugate suppression antinotch filter, antinotch filter followed by moving average filter and harmonic suppression antinotch filter are proposed to improve the identification accuracy. Conjugate suppression antinotch filter suppresses the conjugate frequency component, antinotch filter followed by moving average filter reduces the background noise and harmonic suppression antinotch filter suppresses the harmonic frequency component. Several existing DNA to numerical mapping techniques are compared for GENSCAN test set and based on the result one mapping technique is recommended so that detailed analysis can be performed using various datasets. The computational complexity of the antinotch filters is evaluated in comparison with the ST-DFT method and it is found that the computational load is reduced to a greater extent in antinotch filter. The identification accuracy of the proposed antinotch filter methods is compared with the existing antinotch filter method at the nucleotide level for benchmark datasets. The results show that proposed methods outperform the existing method, giving improved identification of the protein coding regions.