S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-410, 1990.
DOI : 10.1016/S0022-2836(05)80360-2

S. F. Altschul, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-3402, 1997.
DOI : 10.1093/nar/25.17.3389

C. André, P. Vincens, J. Boisvieux, and S. Hazout, MOSAIC: segmenting multiple aligned DNA sequences, Bioinformatics, vol.17, issue.2, pp.196-197, 2001.
DOI : 10.1093/bioinformatics/17.2.196

M. A. Ansari-lari, Comparative sequence analysis of a generich cluster at human chromosome 12p13 and its synthetic region in mouse chromosome 6, Genome Res, vol.8, pp.29-40, 1998.

D. L. Baillie and A. M. Rose, WABA Success: A Tool for Sequence Comparison between Large Genomes, Genome Research, vol.10, issue.8, pp.1071-1073, 2000.
DOI : 10.1101/gr.10.8.1071

R. J. Britten, Precise sequence complementarity between yeast chromosome ends and two classes of just-subtelomeric sequences, Proc. Natl. Acad. Sci. USA, pp.5906-5912, 1998.
DOI : 10.1093/oxfordjournals.molbev.a025712

D. Charlesworth, B. Charlesworth, and G. A. Mcvean, Genome sequences and evolutionary biology, a two-way interaction, Trends in Ecology & Evolution, vol.16, issue.5, pp.235-242, 2001.
DOI : 10.1016/S0169-5347(01)02126-7

J. M. Claverie, Computational methods for the identification of genes in vertebrate genomic sequences, Human Molecular Genetics, vol.6, issue.10, pp.1735-1744, 1997.
DOI : 10.1093/hmg/6.10.1735

M. Crochemore and M. Sagot, Motifs in sequences: localization and extraction, Handbook of Computational Chemistry, 2002.
URL : https://hal.archives-ouvertes.fr/hal-00620799

M. Crochemore and R. Verin, Zones of low entropy in genomic sequences, Computers & Chemistry, vol.23, issue.3-4, pp.275-282, 1999.
DOI : 10.1016/S0097-8485(99)00009-1
URL : https://hal.archives-ouvertes.fr/hal-00619589

A. G. De-brevern and S. Hazout, Hybrid Protein Model (HPM): a method to compact protein 3D-structure information and physicochemical properties, Proceedings Seventh International Symposium on String Processing and Information Retrieval. SPIRE 2000, pp.49-54, 2000.
DOI : 10.1109/SPIRE.2000.878179

A. G. De-brevern and S. Hazout, Compacting local protein folds with a "hybrid protein model", Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), vol.106, issue.1-2, pp.36-47, 2001.
DOI : 10.1007/s002140000227

A. L. Delcher, Alignment of whole genomes, Nucleic Acids Research, vol.27, issue.11, pp.2369-2376, 1999.
DOI : 10.1093/nar/27.11.2369

P. J. Deschavanne, A. Giron, J. Vilain, G. Fagot, and B. Fertil, Genomic signature: characterization and classification of species assessed by chaos game representation of sequences, Molecular Biology and Evolution, vol.16, issue.10, pp.1391-1399, 1999.
DOI : 10.1093/oxfordjournals.molbev.a026048

J. A. Eisen, J. F. Heidelberg, O. White, and S. L. Salzberg, Evidence for symmetric chromosomal inversions around the replication origin in bacteria, Genome Biol, vol.1, pp.1-9, 2000.

L. Florea, Web-based visualization tools for bacterial genome alignments, Nucleic Acids Research, vol.28, issue.18, pp.3486-3496, 2000.
DOI : 10.1093/nar/28.18.3486

A. Force, Preservation of duplicate genes by complementary, degenerative mutations, Genetics, vol.151, pp.1531-1545, 1999.

J. Gouzy, F. Corpet, and D. Kahn, Whole genome protein domain analysis using a new method for domain clustering, Computers & Chemistry, vol.23, issue.3-4, pp.333-340, 1999.
DOI : 10.1016/S0097-8485(99)00011-X
URL : https://hal.archives-ouvertes.fr/hal-00428430

R. C. Hardison, J. Oeltjen, and W. Miller, Long human ? mouse sequence alignments reveal novel regulatory elements: a reason to sequence the mouse genome, Genome Res, vol.7, pp.959-966, 1997.

J. A. Hartigan and M. A. Wong, Algorithm AS 136: A K-Means Clustering Algorithm, Applied Statistics, vol.28, issue.1, pp.100-108, 1979.
DOI : 10.2307/2346830

T. Itoh, K. Takemoto, H. Mori, and T. Gojobori, Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes, Molecular Biology and Evolution, vol.16, issue.3, pp.332-346, 1999.
DOI : 10.1093/oxfordjournals.molbev.a026114

N. Jareborg and R. Durbin, Alfresco---A Workbench for Comparative Genomic Sequence Analysis, Genome Research, vol.10, issue.8, pp.1148-1157, 2000.
DOI : 10.1101/gr.10.8.1148

B. Kapanadze, Comparative sequence analysis of a region on human chromosome 13ql4, frequently deleted in b-cell chronic lymphocytic leukemia, and its homologous region on mouse chromosome 14, Genomics, vol.15, pp.327-334, 2000.

B. F. Kingham, The genome of herpesvirus of turkeys: comparative analysis with Marek???s disease viruses, Journal of General Virology, vol.82, issue.5, pp.1123-1135, 2001.
DOI : 10.1099/0022-1317-82-5-1123

T. Kohonen, An introduction to neural computing, Neural Networks, vol.1, issue.1, pp.3-16, 1989.
DOI : 10.1016/0893-6080(88)90020-2

R. Kolpakov and G. Kucherov, Finding repeats with fixed gap, Proceedings Seventh International Symposium on String Processing and Information Retrieval. SPIRE 2000, pp.115-125, 2000.
DOI : 10.1109/SPIRE.2000.878192
URL : https://hal.archives-ouvertes.fr/inria-00107855

L. Fleche and P. , A tandem repeats database for bacterial genomes: application to the genotyping of Yersinia pestis and Bacillus anthracis, BMC Microbiol, vol.1, issue.2, 2001.
URL : https://hal.archives-ouvertes.fr/hal-01158341

M. Lynch and A. Force, The probability of duplicate gene preservation by sub functionalization, Genetics, vol.154, pp.459-473, 2000.

L. Marsan and M. Sagot, Extracting structured motifs using a suffix tree---algorithms and application to promoter consensus identification, Proceedings of the fourth annual international conference on Computational molecular biology , RECOMB '00, 2000.
DOI : 10.1145/332306.332553
URL : https://hal.archives-ouvertes.fr/hal-00427093

B. Morgenstern, A space-efficient algorithm for aligning large genomic sequences, Bioinformatics, vol.16, issue.10, pp.948-949, 2000.
DOI : 10.1093/bioinformatics/16.10.948

W. R. Pearson and D. J. Lipman, Improved tools for biological sequence comparison., Proc. Natl. Acad. Sci. USA, pp.2444-2448, 1988.
DOI : 10.1073/pnas.85.8.2444
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC280013/pdf

E. P. Rocha, A. Danchin, and A. Viari, Analysis of long repeats in bacterial genomes reveals alternative evolutionary mechanisms in Bacillus subtilis and other competent prokaryotes, Molecular Biology and Evolution, vol.16, issue.9, pp.1219-1230, 1999.
DOI : 10.1093/oxfordjournals.molbev.a026212

M. F. Sagot and E. W. Myers, Identifying Satellites and Periodic Repetitions in Biological Sequences, Journal of Computational Biology, vol.5, issue.3, pp.539-553, 1998.
DOI : 10.1089/cmb.1998.5.539
URL : https://hal.archives-ouvertes.fr/hal-00428496

S. Schwartz, PipMaker---A Web Server for Aligning Two Genomic DNA Sequences, Genome Research, vol.10, issue.4, pp.577-586, 2000.
DOI : 10.1101/gr.10.4.577
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC310868

P. Vincens, A strategy for finding regions of similarity in complete genome sequences, Bioinformatics, vol.14, issue.8, pp.715-725, 1998.
DOI : 10.1093/bioinformatics/14.8.715

Y. Wang and X. Gu, Evolutionary Patterns of Gene Families Generated in the Early Stage of Vertebrates, Journal of Molecular Evolution, vol.51, issue.1, pp.88-96, 2000.
DOI : 10.1007/s002390010069

I. Yanai, C. J. Camacho, and C. Delisi, Predictions of Gene Family Distributions in Microbial Genomes: Evolution by Gene Duplication and Modification, Physical Review Letters, vol.85, issue.12, pp.2641-2644, 2000.
DOI : 10.1103/PhysRevLett.85.2641