Prediction of protein coding regions in DNA sequences using signal processing methods

Identification of protein-coding regions in Deoxyribonucleic Acid (DNA) sequences because of their 3-base periodicity has been a challenging issue in bioinformatics. Many DSP (Digital Signal Processing) techniques have been applied for identification task and concentrated on assigning numerical valu...

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Bibliographic Details
Main Authors: Saberkari, H., Shamsi, M., Sedaaghi, M., Golabi, F.
Format: Conference Proceeding
Language:English
Subjects:
DFT
DNA sequence
exon
notch filter
protein coding region
signal processing
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Summary:Identification of protein-coding regions in Deoxyribonucleic Acid (DNA) sequences because of their 3-base periodicity has been a challenging issue in bioinformatics. Many DSP (Digital Signal Processing) techniques have been applied for identification task and concentrated on assigning numerical values to the symbolic DNA sequence and then applying spectral analysis tools such as the short-time discrete Fourier transform (ST-DFT) to locate periodicity components. In this paper, we investigate the location of exons in DNA strand using directly the DFT approach. By using this method, we see that background noise in the period-3 DNA spectrum has been present. In order to eliminate this noise and for improve the quality of detection, we use an efficient algorithm based on notch filter. Simulation results represent that by using this simple algorithm, the exon location in DNA sequence can be detected as well as possible and the background noise is removes. In this paper, we have also developed a useful user friendly package to analyze DNA sequences.
DOI:10.1109/ISIEA.2012.6496660