Phylogenetic analysis of polyomaviruses based on their complete genomes

Anh, Vo, Chu, K, Li, C, Yu, Zu-Guo, & Zhou, Li-Qian (2008) Phylogenetic analysis of polyomaviruses based on their complete genomes. In Kellenberger, P (Ed.) Natural Computation, 2008. ICNC '08. Fourth International Conference on, IEE Computer Society, China, Shandong, Jinan, pp. 80-84.

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Abstract

Perez-Losada et al. [1] analyzed 72 complete genomes corresponding to nine mammalian (67 strains) and 2 avian (5 strains) polyomavirus species using maximum likelihood and Bayesian methods of phylogenetic inference. Because some data of 2 genomes in their work are now not available in GenBank, in this work, we analyze the phylogenetic relationship of the remaining 70 complete genomes corresponding to nine mammalian (65 strains) and two avian (5 strains) polyomavirus species using a dynamical language model approach developed by our group (Yu et al., [26]). This distance method does not require sequence alignment for deriving species phylogeny based on overall similarities of the complete genomes. Our best tree separates the bird polyomaviruses (avian polyomaviruses and goose hemorrhagic polymaviruses) from the mammalian polyomaviruses, which supports the idea of splitting the genus into two subgenera. Such a split is consistent with the different viral life strategies of each group. In the mammalian polyomavirus subgenera, mouse polyomaviruses (MPV), simian viruses 40 (SV40), BK viruses (BKV) and JC viruses (JCV) are grouped as different branches as expected. The topology of our best tree is quite similar to that of the tree constructed by Perez-Losada et al.

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ID Code: 30522
Item Type: Conference Paper
Keywords: Phylogeny of Polyomaviruses, Complete Genomes, Dynamical Language Model, Correlation Distance
DOI: 10.1109/ICNC.2008.297
Subjects: Australian and New Zealand Standard Research Classification > MATHEMATICAL SCIENCES (010000) > STATISTICS (010400) > Biostatistics (010402)
Australian and New Zealand Standard Research Classification > BIOLOGICAL SCIENCES (060000) > BIOCHEMISTRY AND CELL BIOLOGY (060100) > Bioinformatics (060102)
Divisions: Past > QUT Faculties & Divisions > Faculty of Science and Technology
Copyright Owner: Copyright © 2008 IEEE
Deposited On: 12 Feb 2010 12:38
Last Modified: 06 Mar 2015 01:11

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