Abstract
BackgroundThe identification of protein coding regions (exons) in DNA sequences using signal processing techniques is an important component of bioinformatics and biological signal processing. In this paper, a new method is presented for the identification of exonic regions in DNA sequences. This method is based on the cross-correlation technique that can identify periodic regions in DNA sequences.ResultsThe method reduces the dependency of window length on identification accuracy. The proposed algorithm is applied to different eukaryotic datasets and the output results are compared with those of other established methods. The proposed method increased the accuracy of exon detection by 4% to 41% relative to the most common digital signal processing methods for exon prediction.ConclusionsWe demonstrated that periodic signals can be estimated using cross-correlation. In addition, discrete wavelet transform (DWT) can minimise noise while maintaining the signal. The proposed algorithm, which combines cross-correlation and DWT, significantly increases the accuracy of exonic region identification.
Highlights
The identification of protein coding regions in DNA sequences using signal processing techniques is an important component of bioinformatics and biological signal processing
Our proposed algorithm uses Dmey wavelet to remove noise and thereby increase the accuracy of the exonic region identification
The identification accuracy of our algorithm is fixed for window lengths ranging from 150 to 510 bp, whereas that of the other tested methods depends on window length
Summary
The identification of protein coding regions (exons) in DNA sequences using signal processing techniques is an important component of bioinformatics and biological signal processing. A new method is presented for the identification of exonic regions in DNA sequences. This method is based on the crosscorrelation technique that can identify periodic regions in DNA sequences. When the DNA sequence of a new eukaryotic organism is synthesized, the exonic (protein coding) regions must be distinguished from the introns (see Figure 1 for a schematic of genome arrangement). The existence of a large number of GCA codons in the exonic regions gives greater repetition of G, C and A nucleotides in the first, second and third codon position, respectively.
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