A novel construction of genome space with biological Geometry

DNA Research

Volumn 17, Issue 3, 2010, Pages 155-168

  Yu, Chenglong ^a   Liang, Qian ^b   Yin, Changchuan ^b   He, Rong L ^c   Yau, Stephen S T ^b  

^a CHINESE UNIVERSITY OF HONG KONG   (Hong Kong)

^b UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

^c CHICAGO STATE UNIVERSITY   (United States)

Author keywords

classification; genome space; graphical representation; moment vector; phylogeny

Indexed keywords

DNA;

ARTICLE; BIRD; CORONAVIRUS; DNA SEQUENCE; GENE SEQUENCE; GENE STRUCTURE; GENE VECTOR; GENOME SPACE; GEOMETRY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS; LENTIVIRINAE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; SEVERE ACUTE RESPIRATORY SYNDROME; UNINDEXED SEQUENCE;

ANIMALS; COMPUTATIONAL BIOLOGY; GENOME; HUMANS; LENTIVIRUS; PAN TROGLODYTES; PHYLOGENY; RATS;

AVES; CORONAVIRUS; HUMAN IMMUNODEFICIENCY VIRUS; SARS CORONAVIRUS;

EID: 77955944760     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dsq008     Document Type: Article

References (31)

1. Boore, J.L. and Brown, W.M. 1998, Big tree from little genomes: mitochondrial gene order as a phylogenetic tool, Curr. Opin. Genet. Dev., 8, 668-674
2. Snel, B., Bork, P. and Huynen, M.A. 1999, Genome phy-logeny based on gene content, Nat. Genet., 21, 108-110
3. Kececioglu, J. and Sankoff, D. 1995, Exact and approximation algorithms for the inversion distance, Algorithmica, 13, 180-210.
4. Hannenhalli, S. and Pevzner, P. 1995, Transforming cabbage into turnip. In: Proceedings of the 27th ACM Symposium on Theory of Computing, pp. 178-189
5. Nadeau, J.H. and Sankoff, D. 1998, Counting on comparative maps, Trends Genet., 14, 495-501.
6. Koonin, E.V. 1999, The emerging paradigm and open problems in comparative genomics, Bioinformatics, 15, 265-266
7. Hamori, E. 1985, Novel DNA sequence representation, Nature, 314, 585-586
8. Gates, M.A. 1985, Simpler DNA sequence representations, Nature, 316, 219.
9. Yau, S.S., Wang, J., Niknejad, A., Lu, C., Jin, N. and Ho, Y. 2003, DNA sequence representation without degeneracy, Nucleic Acids Res., 31, 3078-3080
10. Yau, S.S., Yu, C. and He, R. 2008, A protein map and its application, DNA Cell Biol., 27, 241-250
11. Jacobson, N. 1974, Basic Algebra, vol.1. Hindustan Publishing Corporation: India, 135 pp.
12. Jukes, T.H. and Cantor, C.R. 1969, Evolution of protein molecules in mammalian protein metabolism, In: Munro, H.N. and Allison, J.B. (eds.), Mammalian Protein Metabolism, Academic Press: New York, pp. 21-132.
13. Kimura, M. 1980, A simple model for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences, J. Mol. Evol., 16, 111-120
14. Barry, D. and Hartigan, J.A. 1987, Statistical analysis of ominoid molecular evolution, Stat. Sci., 2, 191-210.
15. Lake, J.A. 1994, Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances, Proc. Natl Acad. Sci. USA, 91, 1455-1459
16. Camin, J. and Sokal, R. 1965, A method for deducing branching sequences in phylogeny, Evolution, 19, 311-326
17. Cavalli-Sforza, L.L. and Edwards, A.W.F. 1967, Phylogenetic analysis: models and estimation procedures, Evolution, 21, 550-570
18. Fitch, W.M. 1971, Toward defining the course of evolution: minimum change for a specific tree topology, Syst. Zool., 35, 406-416
19. Felsenstein, J. 1973, Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters, Syst. Zool., 22, 240-249
20. Felsenstein, J. 1981, Evolutionary trees from DNA sequences: a maximum likelihood approach, J. Mol. Evol., 17, 368-376
21. Felsenstein, J. and Churchill, G.A. 1996, A hidden Markov model approach to variation among sites in rate of evolution, Mol. Bio. Evol., 13, 93-104.
22. Brown, W.M., Prager, E.M., Wang, A. and Wilson, A.C. 1982, Mitochondrial DNA sequences of primates: tempo and mode of evolution, J. Mol. Evol., 18, 225-239
23. Kumar, S., Nei, M., Dudley, J. and Tamura, K. 2008, MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences, Brief. Bioinform., 9, 299-306.
24. Raina, S.Z., Faith, J.J., Disotell, T.R., Seligmann, H., Stewart, C.B. and Pollock, D.D. 2005, Evolution of base-substitution gradients in primate mitochondrial genomes, Genome Res., 15, 665-673
25. Rambaut, A., Posada, D., Crandall, K.A. and Holmes, E.C. 2004, The causes and consequences of HIV evolution, Nat. Rev. Genet., 5, 52-61.
26. Gao, F., Bailes, E., Robertson, D.L., et al. 1999, Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes, Nature, 397, 436-441
27. van der Hoek, L., Pyrc, K., Jebbink, M.F., et al. 2004, Identification of a new human coronavirus, Nat. Med., 10, 368-373
28. Guan, Y., Zheng, B.J., He, Y.Q., et al. 2003, Isolation and characterization of viruses related to the SARS corona-virus from animals in southern China, Science, 302, 276-278
29. Wang, M., Yan, M., Xu, H., et al. 2005, SARS-CoV infection in a restaurant from palm civet, Emerg. Infect. Dis., 11, 1860-1865
30. Woo, P.C., Lau, S.K., Chu, C.M., et al. 2005, Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia, J. Virol., 79, 884-895
31. Sankoff, D. and Nadeau, H.J. 2003, Chromosome rearrangements in evolution: From gene order to genome sequence and back, Proc. Natl Acad. Sci. USA, 100, 11188-11189