A novel method to reconstruct phylogeny tree based on thechaos game representation

Na-Na Li, Feng Shi, Xiao-Hui Niu, Jing-Bo Xia

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DOI: 10.4236/jbise.2009.28084                

Abstract

We developed a new approach for the reconstruction of phylogeny trees based on the chaos game representation (CGR) of biological sequences. The chaos game representation (CGR) method generates a picture from a biological sequence, which displays both local and global patterns. The quantitative index of the biological sequence is extracted from the picture. The Kullback-Leibler discrimination information is used as a diversity indicator to measure the dissimilarity of each pair of biological sequences. The new method is inspected by two data sets: the Eutherian orders using concatenated H-stranded amino acid sequences and the genome sequence of the SARS and coronavirus. The phylogeny trees constructed by the new method are consistent with the commonly accepted ones. These results are very promising and suggest more efforts for further developments.

Keywords

CGR (Chaos Game Representation); Discrimination Information; Phylogeny Tree

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	G. H. Gonnet. (1994) New algorithms for the compu- tation of evolutionary phylogenetic trees [M], Com- putationalMethods in Genome Research (Suhai, S., ed.), Plenum, New York, 153–161.
[2]	L. L. Cavalli Sforza and A. W. Edwards. (1967) Phy- logenetic analysis: Models and estimation procedures [J], Genetics, 19(3), 233–257.
[3]	J. Felesenstein. (1981) Evolutionary trees from DNA sequences: A maximum likelihood approach [J], J Mol Evol, 17(6), 368–376.
[4]	L. Jin and M. Nei. (1990) Limitation of the evolution parsimony method of phylogenetic analysis [J], Mol Biol Evol, 7(1), 82–102.
[5]	R. R. Sokal and C. D. Michener. (1958). A statistical method for evaluating systematic relationships [J], Univ. Kans. Sci. Bull, 28, 1409–1438.
[6]	Chris. (2004) Fitch-Margoliash algorithm for calculating the branch lengths [EB/OL], http://www.bioinfo.rpi.edu/~bystrc/courses/biol4540/lecture12/sld002.htm.
[7]	N. Saitou and M. Nei. (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees [J], Molecular Biology and Evolution, 4(4), 406– 425.
[8]	S. Basu, A. Pan, C. Dutta and J. Das. (1997) Chaos game representation of protein, J. Mol. Graphics Model, 15, 279–289.
[9]	H. J. Jeffrey. (1990) Chaos game representation of gene structure [J], Nucleic AcidsRes., 18, 2163–2170.
[10]	Y. Cao, N. Okada, and M. Hasegawa. (1997) Phylo- genetuc position of guinea pigs revisited [J], Mol. Biol. Evol., 14, 461–464.
[11]	M. A. Marra, S. J. Jones, C. R. Astell, et al. (2003) The genome sequence of the SARS-associated coronavirus [J], Science, 300(5624), 1399–1404.
[12]	Y. J. Ruan, C. L. Wei, L. A. Ee, et al. (2003) Com- parative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection [J], The Lancet, 361(9371), 1779–1785.
[13]	P. A. Rota, M. S. Oberste, S. S. Monroe, et al. (2003) Characterization of a novel coronavirus associated with severe acute respiratory syndrome [J], Science, 300 (5624), 1394–1399.
[14]	T. G. Ksiazek, D. Erdman, C. Goldsmith, et al. (2003) A novel coronavirus associated with severe acute respiratory syndrome [J], N Engl J Med, 348(20), 1953–1966.