Fractal and dynamical language methods to construct phylogenetic tree based on protein sequences from complete genomes

Lecture Notes in Computer Science

Volumn 3612, Issue PART III, 2005, Pages 337-347

  Yu, Zu Guo ^a,b   Anh, Vo ^a   Zhou, Li Quan ^b  

^a QUEENSLAND UNIVERSITY OF TECHNOLOGY   (Australia)

^b XIANGTAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

FRACTALS; GENES; NATURAL FREQUENCIES; PROTEINS; TREES (MATHEMATICS);

FRACTAL GEOMETRY; MULTIPLICATIVE MODELS; PHYLOGENETIC TREES; PHYLOGENETICITY;

GENETIC ENGINEERING;

EID: 26844494956     PISSN: 03029743     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1007/11539902_40     Document Type: Conference Paper

References (37)

1. Anh V. V., Lau K. S. and Yu Z. G., Recognition of an organism from fragments of its complete genome, Phys. Rev. E, 66 (2002) 031910
2. rd Edition), CHAPMAN & Hall, London (1998).
3. Brown, J.R., Doolittle.W.F., Archaea and the prokaryote-to-eukaryote transition, Microbiol. Mol. Biol. Rev. 61 (1997) 456-502.
4. Charlebois R.L., R.G. Beiko and M. A. Ragan, Branching out. Nature, 421 (2003) 217-217.
5. Chatton, E., Titres et travaux scientifiques (Seite, Sottano, Italy) (1937).
6. Chu K.H., J. Qi, Z.G. Yu and V.V. Anh, Origin and Phytogeny of Chloroplasts revealed by a simple correlation analysis of complete genome. Mol. Biol. Evol., 21 (2004) 200-206.
7. Doolittle, R.F., Microbial genomes opened up. Nature, 392 (1998) 339-342.
8. Doolittle, R.F., Phylogenetic classification and the universal tree. Science, 284 (1999) 2124-2128.
9. Eisen, J.A. and C.M. Fraser, Phylogenomics: intersection of evolution and genomics. Science, 300 (2003) 1706-1707.
10. Felsenstein,J. PHYLIP (phylogeny Inference package) version 3.5c. Distributed by the author at http://evolution.genetics.washington.edu/phylip. html, (1993).
11. Fitch, W. M., and E. Margoliash, Construction of phylogenetic trees. Science 155 (1967) 279-284.
12. Fitz-Gibbon, S. T., and C. H. House, Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Res., 27 (1999) 4218-4222.
13. Gupta, R.S., Protein phytogenies and signature sequences: A reappraisal of evolutionary relationships among Archaebacteria, Eubacteria, and Eukaryotes. Microbiol. Mol. Biol. Rev., 62 (1998) 1435-1491.
14. Iwabe, N. et al., Evolutionary relationship of archaebacteria, eubacteria and eukaryotes inferred from phylogenetic trees of duplicated genes, Proc. Natl. Acad. Sci. USA, 86 (1989) 9355-9359.
15. Li, M., J. H. Badger, X. Chen, S. Kwong, P. Kearney, and H. Zhang, An information-based sequence distance and its application to whole mitochondrial genome phylogeny. Bioinformatics, 17 (2001) 149-154.
16. Lin, J., and M. Gerstein, Whole-genome trees based on the occurrence of folds and orthologs, implications for comparing genomes at different levels. Genome Res., 10 (2000) 808-818.
17. Martin, W., and R. G. Herrmann, Gene transfer from organelles to the nucleus: How much, what happens, and why? Plant Physiol., 118 (1998) 9-17.
18. Mayr, E., Two empires or three, Proc. Natl. Acad. Sci. U.S.A., 95 (1998) 9720-9723.
19. Qi,J., H. Luo, and B. Hao, CVTree: a phylogenetic tree reconstruction tool based on whole genomes. Nucleic Acids Research, 32 (2004a) W45-W47.
20. Qi, J., B. Wang, and B. Hao, Whole proteome prokaryote phylogeny without sequence alignment: a K-string composition approach. J. Mol. Evol., 58 (2004b) 1-11.
21. Ragan M.A., Detection of lateral gene transfer among microbial genomes. Curr. Opin. Gen. Dev., 11 (2001)620-626.
22. Saitou, N., and M. Nei, The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4 (1987) 406-425.
23. Sankoff, D., G. Leaduc, N. Antoine, B. Paquin, B. F. Lang, and R. Cedergren, Gene order comparisons for phylogenetic inference: Evolution of the mitochondrial genome. Proc. Natl. Acad. Sci. U.S.A., 89 (1992) 6575-6579.
24. Stuart, G. W., K. Moffet, and S. Baker, Integrated gene species phylogenies from unaligned whole genome protein sequences. Bioinformatics, 18 (2002a) 100-108.
25. Stuart, G.W., K.Moffet, and J.J. Leader, A comprehensive vertebrate phylogeny using vector representations of protein sequences from whole genomes. Mol. Biol. Evol., 19 (2002b) 554-562.
26. Tekaia, F., A. Lazcano, and B. Dujon, The genomic tree as revealed from whole proteome comparisons. Genome Res., 9 (1999) 550-557.
27. Vrscay, E.R., in Fractal Geometry and analysis, Eds, Belair, J., (NATO ASI series, Kluwer Academic Publishers) (1991).
28. Weiss, O., M. A. Jimenez, and H. Herzel, Information content of protein sequences. J. Theor. Biol., 206 (2000) 379-386.
29. Woese, C.R., Bacterial evolution, Microbiol. Rev., 51 (1987) 221-271.
30. Woese C.R., The universal ansestor, Proc. Natl. Acad. Sci. USA, 95 (1998) 6854-6859.
31. Woese, C.R., Kandler, O. & Wheelis, M.L., Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya, Proc. Natl. Acad. Sci. USA, 87 (1990) 4576-4579.
32. Yu, Z.G., V.Anh, Phylogenetic tree of prokaryotes based on complete genomes using fractal and correlation analyses, in Proceedings of the Second Asia-Pacific Bioinformatics Conference, Dunedin, New Zealand. (The Australian Computer Society Inc.) (2004).
33. Yu, Z.G., and P. Jiang, Distance, correlation and mutual information among portraits of organisms based on complete genomes. Phys. Lett. A, 286 (2001) 34-46.
34. Yu, Z.G., V. Anh and K. S. Lau, Multifractal and correlation analysis of protein sequences from complete genome. Phys. Rev. E., 68 (2003a) 021913.
35. Yu, Z.G., V. Anh and K. S. Lau, Chaos game representation, and multifractal and correlation analysis of protein sequences from complete genome based on detailed HP model. J. Theor. Biol. 226 (2004) 341-348
36. Yu, Z.G., V. Anh, K.S. Lau and K. H. Chu, The genomic tree of living organisms based on a fractal model. Phys. Lett. A, 317 (2003b) 293-302.
37. Yu,Z.G., L.Q. Zhou, V. V. Anh, K.H. Chu, S.C. Long and J.Q. Deng, Phylogeny of prokaryotes and chloroplasts revealed by a simple composition approach on all protein sequences from whole genome without sequence alignment, J. Mol. Evol. 60 (2005) 538-545.