Journal of Mathematical Chemistry

, Volume 49, Issue 8, pp 1479–1492

Phylogenetic analysis of DNA sequences with a novel characteristic vector

Original Paper

DOI: 10.1007/s10910-011-9811-x

Cite this article as:
Huang, Y. & Wang, T. J Math Chem (2011) 49: 1479. doi:10.1007/s10910-011-9811-x


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.


Biological sequenceSequence comparisonProbability distributionPhylogenetic tree

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  1. 1.School of Mathematical SciencesDalian University of TechnologyDalianPeople’s Republic of China
  2. 2.Department of Mathematics & PhysicsShandong Jiaotong UniversityJinanPeople’s Republic of China