A Novel Graphical and Numerical Representation for Analyzing DNA Sequences Based on Codons

One important task in the study of genome sequences and mutations is to determine densities of specific nucleotides and codons. The graphical representation of DNA sequences provide a simple way of viewing, storing, and comparing various sequences. In this paper, we first present for each kind of codon, a numerically representation as a 2D coordinate (x,y) and give a 2D graphical representation for DNA sequences. Then we transform the graphical representation into a Matrix to facilitate quantitative comparisons of DNA sequences and compute "ALE-index" for this matrix. It is an invariant of DNA sequences and using this index, we construct similarity/dissimilarity table based on this invariant for sequences of DNA of the first exon of beta-globin gene from nine species for illustrating the utility of this representation.