Copyright © 2003 BioChem Press A Simple Method for Characterization and Similarity Analysis of DNA Sequences

Motivation. DNA sequencing has resulted in an abundance of data on DNA sequences for various species. Hence, characterizations and comparisons of sequences become more important but still difficult tasks. The motivation of this paper is to introduce a simple method to characterize and compare the DNA sequences. Method. First, based on three classifications of the four nucleic acid bases, we convert a DNA sequence into three binary sequences. Then, we associate each binary sequence with a G E b b matrix by giving a 2-D ladder-like graphical representation, and thus obtain a 3-component vector whose entries are the normalized matrix norms. By the introduced vector, similarity analysis is made among the coding sequences of the exon I of beta-globin gene of eleven species. Results. As a result, we find that the most similar species are associated with the pairs human-Gorilla, human-Chimpanzee, and Gorilla-Chimpanzee, while gallus shows great dissimilarity with others among the eleven species. This is coincident with the results reported in other literature. Conclusions. From these findings, the main conclusion we can draw is that the 3-component vector has captured important features of the DNA sequences. In addition, our method is so simple that it can be directly extended to deal with long DNA sequences