Advanced DNA Mapping Schemes for Exon Prediction Using Digital Filters

Genomic signal processing (GSP) is the engineering area concerned with genomic data analysis using digital signal processing techniques by conversion of the genomic sequence into numerical one as a first step. One of the central issues in GSP is maximizing the accuracy of protein coding region prediction in a given DNA sequence. In this study advanced DNA numerical representations (genetic code context, 2-bit binary and EIIP) were compared in terms of their sensitivity, specificity and correlation coefficient for maximizing the accuracy of the prediction of protein coding region. Digital filters based technique has been applied to extract the period 3 components and removing the undesired noise from the DNA sequence. Results from implementation of the technique on 8 human genes showed that the 2-bit binary representation scheme associated with the used filtering technique has the maximum accuracy compared to the other tested schemes. These findings suggests that the 2-bit binary representation scheme greatly enhances the prediction accuracy of the protein coding region using digital filters opening a new avenue to use this scheme in different applications.

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