A fast algorithm for exonic regions prediction in DNA sequences

• Main Authors: Hamidreza Saberkari, Mousa Shamsi, Hamed Heravi, Mohammad Hossein Sedaaghi
• Format: Article
• Language: English
• Published: Wolters Kluwer Medknow Publications 2013-01-01
• Series: Journal of Medical Signals and Sensors
• Subjects: Algorithm; DNA sequence; discrete wavelet transform; Exon; Goertzel; protein coding region; signal processing
• Online Access: http://www.jmss.mui.ac.ir/article.asp?issn=2228-7477;year=2013;volume=3;issue=3;spage=139;epage=149;aulast=Saberkari

The main purpose of this paper is to introduce a fast method for gene prediction in DNA sequences based on the period-3 property in exons. First, the symbolic DNA sequences were converted to digital signal using the electron ion interaction potential method. Then, to reduce the effect of background noise in the period-3 spectrum, we used the discrete wavelet transform at three levels and applied it on the input digital signal. Finally, the Goertzel algorithm was used to extract period-3 components in the filtered DNA sequence. The proposed algorithm leads to decrease the computational complexity and hence, increases the speed of the process. Detection of small size exons in DNA sequences, exactly, is another advantage of the algorithm. The proposed algorithm ability in exon prediction was compared with several existing methods at the nucleotide level using: (i) specificity - sensitivity values; (ii) receiver operating curves (ROC); and (iii) area under ROC curve. Simulation results confirmed that the proposed method can be used as a promising tool for exon prediction in DNA sequences.