Analysis of Similarity/Dissimilarity of DNA Primary Sequences Based on Condensed Matrices and Information Entropies

The primary sequence of DNA is a sequence of nucleotides over the four-letters alphabet {A, C, G, T}. Characteristic sequences of a DNA sequence are given in term of classification of bases of nucleotides. Using the characteristic sequences, we construct a set of 3 x 8 matrices and a set of 2 x 2 matrices to represent DNA primary sequences and define the information entropy, which is based on counting all triplets of characteristic sequences. Similarity and dissimilarity analysis based on the condensed matrices and the information entropies are given for the first exon of beta-globin genes sequences belonging to eleven different species.