Gene teams: a new formalization of gene clusters for comparative genomics

Aude, 1999, Applications of the pyramidal clustering method to biological objects, Comput. Chem., 23, 303, 10.1016/S0097-8485(99)00006-6 Bansal, 1999, An automated comparative analysis of 17 complete microbial genomes, Bioinformatics, 15, 900, 10.1093/bioinformatics/15.11.900 Barloy-Hubler, 2001, Ribosomal protein gene cluster analysis in eubacterium genomics: homology between Sinorhizobium meliloti strain 1021 and Bacillus subtilis, Nucl. Acids Res., 29, 2747, 10.1093/nar/29.13.2747 Bergeron, 2002, The algorithmic of gene teams, 464 Comet, 1999, Significance of Z-Value statistics of Smith–Waterman scores for protein alignements, Comput. Chem., 23, 317, 10.1016/S0097-8485(99)00008-X Deckert, 1998, The complete genome of the hyperthermophilic bacterium Aquifex aeolicus, Nature, 26, 353, 10.1038/32831 Fujibuchi, 2000, Automatic detection of conserved gene clusters in multiple genomes by graph comparison and p-quasi grouping, Nucleic Acids Res., 28, 4029, 10.1093/nar/28.20.4029 Gale, 1998, Plant comparative genetics after 10 years, Science, 23, 656, 10.1126/science.282.5389.656 Glemet, 1997, lassap, a Large Scale Sequence Comparison Package, CABIOS, 13, 137 Heber, 2001, Algorithms for finding gene clusters, 252 Heber, 2001, Finding all common intervals of k permutations, 207 Korbel, 2002, SHOT: a web server for the construction of genome phylogenies, Trends Genet., 18, 158, 10.1016/S0168-9525(01)02597-5 Ogata, 2000, A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters, Nucl. Acids Res., 28, 4021, 10.1093/nar/28.20.4021 Overbeek, 1999, The use of gene clusters to infer functional coupling, Proc. Natl. Acad. Sci. USA, 96, 2896, 10.1073/pnas.96.6.2896 Remm, 2001, Automatic clustering of orthologs and in-paralogs from pairwise species comparisons, J. Mol. Biol., 314, 1041, 10.1006/jmbi.2000.5197 Sankoff, 2002, Short inversions and conserved gene clusters, Bioinformatics, 18, 1305, 10.1093/bioinformatics/18.10.1305 Sankoff, 1992, Gene order comparisons for phylogenetic inference: evolution of the mitochondrial genome, Proc. Natl. Acad. Sci. USA, 89, 6575, 10.1073/pnas.89.14.6575 Snel, 2002, The identification of functional modules from the genomic association of genes, Proc. Natl. Acad. Sci. USA, 99, 5890, 10.1073/pnas.092632599 Tatusov, 2000, The COG database: a tool for genome-scale analysis of protein functions and evolution, Nucleic Acids Res., 28, 33, 10.1093/nar/28.1.33 Uno, 2000, Fast algorithms to enumerate all common intervals of two permutations, Algorithmica, 26, 290, 10.1007/s004539910014