Walsh code based numerical mapping method for the identification of protein coding regions in eukaryotes

Abstract

The protein coding regions play a significant role for gene applications in genomic signal processing. Unlike prokaryotes, the coding regions in eukaryotes are arranged in a random manner. Owing to unequal lengths and low volume density of coding regions, the identification of coding regions makes cumbersome. In this work, a new numerical mapping method based on Walsh codes is proposed to detect the coding regions in eukaryotes. The Walsh code for each nucleotide is obtained using the statistical features of a DNA sequence. The proposed method uses static type of mapping to convert a string of DNA nucleotides into a numerical sequence. The numerical sequence is given as an input to the digital signal processing based spectrum identification tool to detect the existence of quasi-periodic components within the coding region. The advantage of our method is that it is simple to design and easy to represent. The performance of the proposed method has been tested on four benchmark databases and a random set of sequences collected from the National Center for Biological Information (NCBI) database. Furthermore, it has been compared with other state-of-the-art spectrum based numerical mapping methods for statistical features such as sensitivity, specificity and accuracy. The proposed method is efficient as it attains 94 % accuracy, 85 % sensitivity and 96 % specificity when tested on the benchmark C. Elegans gene sequence.