A unified approach for reconstructing ancient gene clusters

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 6, Issue 3, 2009, Pages 387-400

  Stoye, Jens ^a   Wittler, Roland ^a  

^a BIELEFELD UNIVERSITY   (Germany)

Author keywords

Comparative genomics; Consistency; Gene cluster; Gene cluster reconstruction; Gene order; Parsimony; Phylogeny

Indexed keywords

COMPARATIVE GENOMICS; CONSISTENCY; GENE CLUSTER; GENE CLUSTER RECONSTRUCTION; GENE ORDER; PARSIMONY; PHYLOGENY;

BIOLOGY; LABELS; OPTIMIZATION;

GENES;

BIOLOGY; DATA; EFFICIENCY; GENES; LABELS; OPTIMIZATION; PROBLEM SOLVING; SIMULATION;

ALGORITHM; ARTICLE; BACTERIAL GENOME; BACTERIUM; BIOLOGICAL MODEL; COMPUTER SIMULATION; GENE ORDER; GENETICS; GENOMICS; METHODOLOGY; MULTIGENE FAMILY; PHYLOGENY;

ALGORITHMS; BACTERIA; COMPUTER SIMULATION; GENE ORDER; GENOME, BACTERIAL; GENOMICS; MODELS, GENETIC; MULTIGENE FAMILY; PHYLOGENY;

EID: 68649092195     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2008.135     Document Type: Article

References (26)

1. T. Dandekar, B. Snel, M. Huynen, and P. Bork, "Conservation of Gene Order: A Fingerprint of Proteins That Physically Interact," Trends in Biochemical Sciences, vol.23, no.9, pp. 324-328, 1998. (Pubitemid 28461862)
2. R. Overbeek, M. Fonstein, M. D'Souza, G.D. Pusch, and N. Maltsev, "The Use of Gene Clusters to Infer Functional Coupling," Proc. Nat'l Academy of Sciences USA, vol.96, no.6, pp. 2896-2901, 1999. (Pubitemid 29148815)
3. X. He and M.H. Goldwasser, "Identifying Conserved Gene Clusters in the Presence of Homology Families," J. Computational Biology, vol.12, no.6, pp. 638-656, 2005. (Pubitemid 41170473)
4. S. Bocker, K. Jahn, J. Mixtacki, and J. Stoye, "Computation of Median Gene Clusters," Proc. 12th Ann. Int'l Conf. Research in Computational Molecular Biology (RECOMB '08), pp. 331-345, 2008.
5. W.C. Lathe III, B. Snel, and P. Bork, "Gene Context Conservation of a Higher Order than Operons," Trends in Biochemical Sciences, vol. 25, no. 10, pp. 474-479, 2000. (Pubitemid 30767774)
6. J. Tamames, "Evolution of Gene Order Conservation in Prokaryotes," Genome Biology, vol.2, pp. research0020.1-research0027.11, 2001.
7. J.G. Lawrence and J.R. Roth, "Selfish Operons: Horizontal Transfer May Drive the Evolution of Gene Clusters," Genetics, vol.143, no.4, pp. 1843-1860, 1996.
8. R. Hoberman and D. Durand, "The Incompatible Desiderata of Gene Cluster Properties," Proc. Third Research in Computational Molecular Biology (RECOMB) Satellite Workshop Comparative Genomics (RECOMB-CG '05), 2005.
9. A. Bergeron, C. Chauve, and Y. Gingras, "Formal Models of Gene Clusters," Bioinformatics Algorithms: Techniques and Applications, Wiley, 2007.
10. A. Bergeron, M. Blanchette, A. Chateau, and C. Chauve, "Reconstructing Ancestral Gene Order Using Conserved Intervals," Proc. Fourth Int'l Workshop Algorithms in Bioinformatics (WABI '04), pp. 14-25, 2004. (Pubitemid 39749994)
11. Z. Adam, M. Turmel, C. Lemieux, and D. Sankoff, "Common Intervals and Symmetric Difference in a Model-Free Phyloge- nomics, with an Application to Streptophyte Evolution," J. Computational Biology, vol.14, no.4, pp. 436-445, 2007. (Pubitemid 46911217)
12. T. Uno and M. Yagiura, "Fast Algorithms to Enumerate All Common Intervals of Two Permutations," Algorithmica, vol.26, no.2, pp. 290-309, 2000.
13. A. Bergeron and J. Stoye, "On the Similarity of Sets of Permutations and Its Applications to Genome Comparison," J. Computational Biology, vol.13, no.7, pp. 1340-1354, 2006. (Pubitemid 46100697)
14. G.M. Landau, L. Parida, and O. Weimann, "Gene Proximity Analysis across Whole Genomes via PQ Trees," J. Computational Biology, vol.12, no.10, pp. 1289-1306, 2005. (Pubitemid 44743644)
15. K.S. Booth and G.S. Lueker, "Testing for the Consecutive Ones Property, Interval Graphs and Graph Planarity Using PQ-Tree Algorithms," J. Computing and System Sciences, vol.13, no.3, pp. 335-379, 1976.
16. W.M. Fitch, "Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology," Systematic Zoology, vol.20, no.4, pp. 406-416, 1971.
17. J.A. Hartigan, "Minimum Mutation Fits to a Given Tree," Biometrics, vol.29, no.1, pp. 53-65, 1973.
18. D. Gusfield, Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology. Cambridge Univ. Press, 1997.
19. L. Parida, Pattern Discovery in Bioinformatics: Theory and Algorithms. Chapman &Hall/CRC, 2007.
20. D.L. Wheeler, C. Chappey, A.E. Lash, D.D. Leipe, T.L. Madden, G. Schuler, T.A. Tatusova, and B.A. Rapp, "Database Resources of the National Center for Biotechnology Information," Nucleic Acids Research, vol.28, no.1, pp. 10-14, 2000. (Pubitemid 30047702)
21. D.A. Benson, I. Karsch-Mizrachi, D.J. Lipman, J. Ostell, B.A. Rapp, and D.L. Wheeler, "Genbank," Nucleic Acids Research, vol.28, no.1, pp. 15-18, 2000. (Pubitemid 30047703)
22. R.L. Tatusov, E.V. Koonin, and D.J. Lipman, "A Genomic Perspective on Protein Families," Science, vol.278, pp. 631-637, 1997.
23. R.L. Tatusov, N.D. Fedorova, J.D. Jackson, A.R. Jacobs, B. Kiryutin, E.V. Koonin, D.M. Krylov, R. Mazumder, S.L. Mekhedov, A.N. Nikolskaya, B.S. Rao, S. Smirnov, A.V. Sverdlov, S. Vasudevan, Y.I. Wolf, J.J. Yin, and D.A. Natale, "The Cog Database: An Updated Version Includes Eukaryotes," BMC Bioinformatics, vol.4, p. 41, 2003. (Pubitemid 38751229)
24. M. Sugitaa, H. Sugishitaa, T. Fujishiroa, M. Tsuboia, C. Sugitaa, T. Endob, and M. Sugiura, "Organization of a Large Gene Cluster Encoding Ribosomal Proteins in the Cyanobacterium Synecho- coccus sp. Strain pcc 6301: Comparison of Gene Clusters among Cyanobacteria, Eubacteria and Chloroplast Genomes," Gene, vol.195, no.1, pp. 73-79, 1997. (Pubitemid 27336964)
25. W.-L. Hsu and R. McConnell, "PC-Trees," Handbook of Data Structures and Applications, D.P. Mehta and S. Sahni, eds., 2003.
26. P.L. Erdos and L.A. Szekely, "On Weighted Multiway Cuts in Trees," Math. Programming, vol.65, no.1, pp. 93-105, 1994.