Phylogenetic analysis of DNA sequences with a novel characteristic vector

In the basic biological research, one of major tasks is to compare biological sequences to infer evolutionary relations among sequences. In this paper, considering both the positions and numbers of a k-word and the random background, a novel characteristic vector of a DNA sequence is proposed to serve for genetic sequences comparison and phylogenetic analysis. The vector is composed of elements which characterize the relative difference of a DNA sequence from a sequence generated by a (k − 2)th order Markov process. Finally, we reconstruct the phylogenetic trees of 48 HEV (Hepatitis E virus) and 20 Eutherian mammals. The results show that this new method provides more information about k-word and improves the efficiency of sequence comparison.

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