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

• Published in: 2012 IEEE Symposium on Industrial Electronics and Applications pp. 355 - 360
• Main Authors: Saberkari, H., Shamsi, M., Sedaaghi, M., Golabi, F.
• Format: Conference Proceeding
• Language: English
• Published: IEEE 01.09.2012
• Subjects: DFT; DNA sequence; exon; notch filter; protein coding region; signal processing
• ISBN: 1467330043; 9781467330046
• DOI: 10.1109/ISIEA.2012.6496660

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.