Homology prediction refinement and reconstruction of gene content and order of ancestral bacterial genomes

2010 ACM International Conference on Bioinformatics and Computational Biology, ACM-BCB 2010

Volumn , Issue , 2010, Pages 230-236

  Yang, Kuan ^a   Setubal, Joao C ^a  

^a VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

Author keywords

Ancestral genome reconstruction; Genomics; Ortholog gene family prediction; Rhizobiales

Indexed keywords

ANCESTRAL GENOMES; BACTERIAL GENOMES; GENE CONTENT; GENE ORDERS; GENOMICS; ORTHOLOGS; PROTEOBACTERIA; REFINEMENT METHODS; RHIZOBIALES; SYNTENY;

BACTERIOLOGY; BIOINFORMATICS; BIOLOGY; FORECASTING; REPAIR;

GENES;

EID: 77958043035     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/1854776.1854810     Document Type: Conference Paper

References (28)

1. Koonin, E.V., Orthologs, Paralogs, and Evolutionary Genomics. Annu. Rev. Genet., 2005. 39: p. 309-38.
2. Fitch, W.M., Distinguishing homologous from analogous proteins. Syst. Zool., 1970. 19(99-106).
3. Heijden, R.T.v.d., et al., Orthology prediction at scalable resolution by phylogenetic tree analysis. BMC Bioinformatics, 2007. 8(83).
4. Snel, B. and M.A. Huynen, Quantifying Modularity in the Evolution of Biomolecular Systems. Genome Research, 2004. 14(3): p. 391-397.
5. Stone, E.A. and A. Sidow, Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity. Genome Research, 2005. 15(7): p. 978-986.
6. Jothi, R., et al., COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations. Bioinformatics, 2006. 22(7): p. 779-788.
7. Storm, C.E.V. and E.L.L. Sonnhammer, Automated ortholog inference from phylogenetic trees and calculation of rothology reliability. Bioinformatics, 2002. 18(92-99).
8. Dufayard, J.-F., et al., Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases. Bioinformatics, 2005. 21(11): p. 2596-3603.
9. Zmasek, C.M. and S.R. Eddy, RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs. BMC Bioinformatics, 2002. 3(14).
10. Koski, L.B. and G.B. Golding, The Closest BLAST Hit Is Often Not the Nearest Neighbor Journal of Molecular Evolution, 2004. 52(6): p. 1432-1432.
11. Remm, M., C.E.V. Storm, and E.L.L. Sonnhammer, Automatic clustering of orthologs and inparalogs from pairwise species comparisons. Journal of Molecular Biology, 2001. 214(5): p. 1041-1052.
12. Li, L., C.J.S. Jr., and D.S. Roos, OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes. Genome Research, 2003. 13(9): p. 2178
13. Hubbard, T.J.P., et al., Ensembl 2007. Nucleic Acids Res., 2007. V35: p. 610-617.
14. Wheeler, D.L., et al., Database resources of the National Center for Biotechnology Information Nucleic Acids Res., 2005. 33: p. D39-D45.
15. Arnold Kuzniar1, R.C.H.J.v.H., Sa'ndor Pongor2 and Jack A.M. Leunissen, The quest for orthologs: finding the corresponding gene across genomes. Trends in Genetics, 2008. 24(11): p. 539-551.
16. Hulsen, T., et al., Benchmarking ortholog identification methods using functional genomics data. 7, 2006: p. R31.
17. Lemoine, F., O. Lespinet, and B. Labedan, Assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data. BMC Evolutionary Biology, 2007. 7(237).
18. Pe'er, I. and R. Shamir, The median problems for breakpoints are NP-complete. Elec Colloq Comput Complexity, 1998: p. 71.
19. Moret, B.M.E., et al., Steps toward accurate reconstructions of phylogenies from gene-order data. Journal of Computer and System Sciences, 2002. 65(3): p. 508-525
20. Caprara, A. Formulations and hardness of multiple sorting by reversals. in In proceedings of the 3rd International Conference of Computational Molecular Biology. 1999. Lyon, France: ACM Press.
21. Moret, B.M.E.T., J. ; Warnow, T. ; Gascuel, O., Reconstructing phylogenies from gene-content and gene-order data. Mathematics of Evolution and Phylogeny. 2005: Oxford University Press.
22. Bourque, G., G. Tesler, and P.A. Pevzner, The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction. Genome Res, 2006. 16(3): p. 311-3.
23. Eriksen, N., Reversal and transposition medians. Theoretical Computer Science, 2007. 374: p. 111-126.
24. Bhutkar, A., W.M. Gelbart, and T.F. Smith, Inferring genome-scale rearrangement phylogeny and ancestral gene order: a Drosophila case study. Genome Biol, 2007. 8(11): p. R236.
25. Boussau, B., et al., Computational inference of scenarios for alpha-proteobacterial genome evolution. Proc Natl Acad Sci U S A, 2004. 101(26): p. 9722-7.
26. Slater, S.C., et al., Genome Sequences of Three Agrobacterium Biovars Help Elucidate the Evolution of Multichromosome Genomes in Bacteria. Journal of Bacteriology, 2009. 191(8): p. 2501-2511.
27. Wu, M. and J.A. Eisen, A simple, fast, and accurate method of phylogenomic inference. Genome Biol. 2008;9(10):R151.
28. Genome Biology, 2008. 9(R151).