Gene team tree: A hierarchical representation of gene teams for all gap lengths

Journal of Computational Biology

Volumn 16, Issue 10, 2009, Pages 1383-1398

  Zhang, Melvin ^a   Leong, Hon Wai ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

Algorithms; Comparative genomics; Gene clusters; Gene order analysis

Indexed keywords

ARTICLE; CHROMOSOME; DATA BASE; GENE CLUSTER; GENE TEAM; GENETIC ALGORITHM; GENETIC CONSERVATION; GENETIC DISTANCE; GENETIC MODEL; GENOME; HUMAN; HUMAN GENOME; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL;

ALGORITHMS; ANIMALS; BACILLUS SUBTILIS; ESCHERICHIA COLI; EVOLUTION, MOLECULAR; GAMMAPROTEOBACTERIA; GENOME; HUMANS; MICE; MODELS, GENETIC; MULTIGENE FAMILY; OPERON; PHYLOGENY;

ESCHERICHIA COLI K12; GAMMAPROTEOBACTERIA;

EID: 70349808217     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2009.0093     Document Type: Article

References (22)

1. Béal, M.-P., Bergeron, A., Corteel, S., et al. 2004. An algorithmic view of gene teams. Theoret. Comput. Sci. 320, 395-418.
2. Bourque, G., Pevzner, P.A., and Tesler, G. 2004. Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes. Genome Res. 14, 507-516.
3. Ermolaeva, M.D., White, O., and Salzberg, S.L. 2001. Prediction of operons in microbial genomes. Nucleic Acids Res. 29, 1216-1221.
4. Fitch, W. 2000. Homology-a personal view on some of the problems. Trends Genet. 16, 227-231.
5. Fu, Z., Chen, X., Vacic, V., et al. 2007. Msoar: a high-throughput ortholog assignment system based on genome rearrangement. J. Comput. Biol. 14, 1160-1175.
6. Gama-Castro, S., Jimnez-Jacinto, V., Peralta-Gil, M., et al. 2008. Regulondb (version 6.0): gene regulation model of Escherichia coli k-12 beyond transcription, active (experimental) annotated promoters and textpresso navigation. Nucleic Acids Res. 36, D120-D124.
7. He, X., and Goldwasser, M.H. 2005. Identifying conserved gene clusters in the presence of homology families. J. Comput. Biol. 12, 638-656.
8. Hoberman, R., and Durand, D. 2005. The incompatible desiderata of gene cluster properties. Lect. Notes Comput. Sci. 3678, 73-87.
9. Hoberman, R., Sankoff, D., and Durand, D. 2005. The statistical analysis of spatially clustered genes under the maximum gap criterion. J. Comput. Biol. 12, 1083-1102.
10. Jaccard, P. 1908. Nouvelles recherches sur la distribution florale. Bull. Soc. Vaudoise Sci. Nat. 44, 223-270.
11. Jacob, F., Perrin, D., Sanchez, C., et al. 1960. Operon: a group of genes with the expression coordinated by an operator. Comptes Rendus Hebdomadaires Seances 'Acad. Sci. 250, 1727.
12. Kim, S., Choi, J.-H., and Yang, J. 2005. Gene teams with relaxed proximity constraint. Proc. 2005 IEEE Comput. Syst. Bioinform. Conf. (CSB'05) 44-55.
13. Lawrence, J. 1999. Selfish operons: the evolutionary impact of gene clustering in prokaryotes and eukaryotes. Curr. Opin. Genet. Dev. 9, 642-648.
14. Lerat, E., Daubin, V., and Moran, N.A. 2003. From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-proteobacteria. PLoS Biol. 1.
15. Ling, X., He, X., Xin, D., et al. 2008. Efficiently identifying max-gap clusters in pairwise genome comparison. J. Comput. Biol. 15, 593-609.
16. McLysaght, A., Hokamp, K., and Wolfe, K. 2002. Extensive genomic duplication during early chordate evolution. Nat. Genet. 31, 200-204.
17. Overbeek, R., Fonstein, M., D'Souza, M., et al. 1999. The use of gene clusters to infer functional coupling. Proc. Natl. Acad. Sci. USA 96, 2896-2901.
18. Parida, L. 2007. Gapped permutation pattern discovery for gene order comparisons. J. comput. Biol. 14, 45-55.
19. Pertea, M., Ayanbule, K., Smedinghoff, M., et al. 2008. OperonDB: a comprehensive database of predicted operons in microbial genomes. Nucleic Acids Res.
20. Snel, B., Bork, P., and Huynen, M.A. 2002. The identification of functional modules from the genomic association of genes. Proc. Natl. Acad. Sci. USA 99, 5890-5895.
21. Tatusov, R.L., Natale, D.A., Garkavtsev, I.V., et al. 2001. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29, 22-28.
22. Uno, T., and Yagiura, M. 2000. Fast algorithms to enumerate all common intervals of two permutations. Algorithmica 26, 290-309.