Efficiently identifying max-gap clusters in pairwise genome comparison

Journal of Computational Biology

Volumn 15, Issue 6, 2008, Pages 593-609

  Ling, Xu ^a   He, Xin ^a   Xin, Dong ^a   Han, Jaiwei ^a  

^a University of Illinois at Urbana Champaign   (United States)

Author keywords

Algorithms; Gene clusters; Gene networks; Recognition of genes; Regulatory elements; Sequence analysis

Indexed keywords

ARTICLE; BACTERIAL GENOME; CONCEPTUAL FRAMEWORK; DNA STRUCTURE; GENE CLUSTER; GENETIC ALGORITHM; GENOME; GENOMICS; MATHEMATICAL COMPUTING; MATHEMATICAL GENETICS; METHODOLOGY; OPERON; PRIORITY JOURNAL; SEQUENCE HOMOLOGY; STATISTICAL ANALYSIS; STATISTICAL MODEL;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; CLUSTER ANALYSIS; GENOME;

BACTERIA (MICROORGANISMS);

EID: 47549083673     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2008.0010     Document Type: Article

References (29)

1. Bergeron, A., Corteel, S., and Raffinot, M. 2002. The algorithmic of gene teams. Proc. WABI '02 464-476.
2. Bourque, G., Zdobnov, E.M., Bork, P., et al. 2005. Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages. Genome Res. 15, 98-110.
3. Calabrese, P., Chakravarty, S., and Vision, T. 2003. Fast identification and statistical evaluation of segmental homologies in comparative maps. Bioinformatics 19, i74-i80.
4. Cannon, S., Kozik, A., Chan, B., et al. 2003. Diaghunter and genopix2d: programs for genomic comparisons, large-scale homology discovery and visualization. Genome Biol. 4, R68.
5. Edwards, M.T., Rison, S.C., Stoker, N.G., et al. 2005. A universally applicable method of operon map prediction on minimally annotated genomes using conserved genomic context. Nucleic Acids Res. 33, 3253-3262.
6. Haas, B., Delcher, A., Wortman, J., et al. 2004. Dagchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics 20, 3643-3646.
7. Hampson, S.E., Gaut, B.S., and Baldi, P. 2005. Statistical detection of chromosomal homology using shared-gene density alone. Bioinformatics 21, 1339-1348.
8. Han, J., Pei, J., Yin, Y., et al. 2003. Mining frequent patterns without candidate generation: a frequent-pattern tree approach. Data Min. Knowl. Discov. 8, 53-87.
9. He, X., and Goldwasser, M.H. 2005. Identifying conserved gene clusters in the presence of homology families. J. Comput. Biol. 12, 638-656.
10. 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.
11. Kim, S., Choi, J.-H., and Yang, J. 2005. Gene teams with relaxed proximity constraint. Proc. CSB '05 44-55,
12. Luc, N., Risler, J.-L., Bergeron, A., et al. 2003. Gene teams: a new formalization of gene clusters for comparative genomics. Comput. Biol. Chem. 27, 59-67.
13. Ma, B., Tromp, J., and Li, M. 2002. Patternhunter: faster and more sensitive homology search. Bioinformatics 18, 440-445.
14. McLysaght, A., Hokamp, K., and Wolfe, K.H. 2002. Extensive genomic duplication during early chordate evolution. Nat. Genet. 31, 200-204.
15. Pei, J., Han, J., Mortazavi-Asl, B., et al. 2001. Prefixspan: mining sequential patterns efficiently by prefix projected pattern growth. Proc. ICDE'01 215-226,
16. Pevzner, P., and Tesler, G. 2003. Genome rearrangements in mammalian evolution: lessons from human and mouse genomic sequences. Genome Res. 13, 37-45.
17. Postlethwait, J.H., Woods, I.G., Phuong, N.-H., et al. 2000. Zebrafish comparative genomics and the origins of vertebrate chromosomes. Genome Res. 10, 1890-1902.
18. Price, M.N., Huang, K.H., Alm, E.J., et al. 2005. A novel method for accurate operon predictions in all sequenced prokaryotes. Nucleic Acids Res. 33, 880-892.
19. Salgado, H., Moreno-Hagelsieb, G., Smith, T.F., et al. 2000. Operons in Escherichia coli: genomic analyses and predictions. Proc. Natl. Acad. Sci. USA 97, 6652-6657.
20. Salgado, H., Gama-Castro, S., Peralta-Gil, M., et al. 2006. Regulondb (version 5.0): Escherichia coli k-12 transcriptional regulatory network, operon organization, and growth conditions. Nucleic Acids Res. 1, D394-D397.
21. Schwartz, S., Kent, W., Smit, A., et al. 2003. Human-mouse alignments with blastz. Genome Res. 13, 103-107.
22. Simillion, C., Vandepoele, K., Van Montagu, M.C.E., et al. 2002. The hidden duplication past of Arabidopsis thaliana. Proc. Natl. Acad. Sci. 99, 13627-13632.
23. Soderlund, C., Nelson, W., Shoemaker, A., et al. 2006. Symap: a system for discovering and viewing syntenic regions of fpc maps. Genome Res. 16, 1159-1168.
24. 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.
25. Vandepoele, K., Saeys, Y., Simillion, C., et al. 2002. The automatic detection of homologous regions (adhore) and its application to microcolinearity between arabidopsis and rice. Genome Res. 12, 1792-1801.
26. Venter, J.C., Adams, M.D., Myers, E.W., et al. 2001. The sequence of the human genome. Science 291, 1304-1351.
27. Wang, X., Shi, X., Li, Z., et al. 2006. Statistical inference of chromosomal homology based on gene colinearity and applications to arabidopsis and rice. BMC Bioinform. 7, 447.
28. Westover, B.P., Buhler, J.D., Sonnenburg, J.L., et al. 2005. Operon prediction without a training set. Bioinformatics 21, 880-888.
29. Zheng, Y., Anton, B.P., Roberts, R.J., et al. 2005. Phylogenetic detection of conserved gene clusters in microbial genomes. BMC Bioinform. 6, 243.