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Huang, Yujuan; Wang, Tianming

Phylogenetic analysis of DNA sequences with a novel characteristic vector. (English) Zbl 1303.92081

J. Math. Chem. 49, No. 8, 1479-1492 (2011).
Summary: 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.

Cited in 2 Documents

MSC:

92D15 Problems related to evolution
92D10 Genetics and epigenetics

Keywords:

biological sequence; sequence comparison; probability distribution; phylogenetic tree

Software:

PHYLIP
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Full Text: DOI

References:

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