Applications of representation method for DNA sequences based on symbolic dynamics

This paper addresses the applications of the improved representation method of DNA sequences based on symbolic dynamics. This method can visualize DNA sequences in three-dimensional coordinates with no loss of information in the transfer of data from a DNA sequence to its mathematical representation, and be applied to solve fundamental problems in bioinformatics fields. Graphical alignment of two shorter DNA sequences is exemplified for the application of the symbolic-dynamics-based representation method to sequence alignment. With the truncated length of DNA representation being chosen as the number of nucleotides in a codon, the application can be then extended to codon alignment. Based on the applications of alignment, the examination of similarities/dissimilarities among the coding sequences of the first exon of β-globin gene of different species illustrates the utility of the improved representation approach.