. Tabela-6, Número de regiões com cobertura abaixo da média identificadas, em cada cromossomo, pelo algoritmo que possui duas etapas de janela deslizante. A primeira etapa utilizou w 1 = 500 e identificou regiões com alta e baixa cobertura ao longo do cromossomo. A segunda etapa processou as regiões identificadas pela primeira etapa e identificou sub-regiões com coberturas de hits menores do que a apresentada pela região que as contém. Os seguintes valores de w 2 foram testados

|. Se and |. , temos um possível candidato a breakpoint e uma das seguintes situações podem ocorrer

G. Achaz, F. Boyer, C. P. Rocha, A. Viari, and E. Coissac, Repseek, a tool to retrieve approximate repeats from large DNA sequences, Bioinformatics, vol.23, issue.1, pp.119-121, 2007.
DOI : 10.1093/bioinformatics/btl519

M. Alekseyev and P. A. Pevzner, Are There Rearrangement Hotspots in the Human Genome?, PLoS Computational Biology, vol.46, issue.11, p.209, 2007.
DOI : 10.1371/journal.pcbi.0030209.sd001

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

L. Andersson, A. Archibald, M. Ashburner, S. Audun, W. Barendse et al., Comparative Genome Organization of Vertebrates, Mammalian Genome, vol.6, issue.10, pp.717-734, 1996.
DOI : 10.1007/s003359900222

I. Auger and C. Lawrence, Algorithms for the optimal identification of segment neighborhoods, Bulletin of Mathematical Biology, vol.25, issue.1, pp.39-54, 1989.
DOI : 10.1007/BF02458835

D. A. Bader, B. M. Moret, and M. Yan, A Linear-Time Algorithm for Computing Inversion Distance between Signed Permutations with an Experimental Study, Journal of Computational Biology, vol.8, issue.5, pp.483-491, 2001.
DOI : 10.1089/106652701753216503

G. Badr, K. Swenson, and D. Sankoff, Listing all parsimonius reversal sequences: New algorithms and perspectives, Proceedings of the 8th Annual RECOMB Satellite Workshop on Comparative Genomics (RECOMB-CG 2010), pp.39-49, 2010.

V. Bafna and P. A. Pevzner, Sorting by reversals: Genome rearrangements in plant organelles and evolutionary history of X chromosome, Molecular Biology and Evolution, vol.12, issue.2, pp.239-246, 1995.

V. Bafna and P. A. Pevzner, Sorting by Transpositions, Proceedings of the Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, pp.614-623, 1995.
DOI : 10.1137/S089548019528280X
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.156.1168

V. Bafna and P. A. Pevzner, Genome Rearrangements and Sorting by Reversals, SIAM Journal on Computing, vol.25, issue.2, pp.272-289, 1996.
DOI : 10.1137/S0097539793250627
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.109.1352

V. Bafna and P. A. Pevzner, Sorting by Transpositions, SIAM Journal on Discrete Mathematics, vol.11, issue.2, pp.224-240, 1998.
DOI : 10.1137/S089548019528280X

A. Bashir, S. Volik, C. Collins, V. Bafna, and B. J. Raphael, Evaluation of Paired-End Sequencing Strategies for Detection of Genome Rearrangements in Cancer, PLoS Computational Biology, vol.25, issue.4, p.1000051, 2008.
DOI : 10.1371/journal.pcbi.1000051.s009

C. Baudet and Z. Dias, Chronological order of reversal events on Rickettsia genus, Proceedings of the International Symposium on Biocomputing, ISB '10, 2010.
DOI : 10.1145/1722024.1722026
URL : https://hal.archives-ouvertes.fr/hal-00748584

C. Baudet and Z. Dias, An improved algorithm to enumerate all traces that sort a signed permutation by reversals, Proceedings of the 2010 ACM Symposium on Applied Computing, SAC '10, 2010.
DOI : 10.1145/1774088.1774416
URL : https://hal.archives-ouvertes.fr/hal-00748579

C. Baudet and Z. Dias, Partial enumeration of solutions traces for the problem of sorting by signed reversals, Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB '11, p.11, 2010.
DOI : 10.1145/2147805.2147884
URL : https://hal.archives-ouvertes.fr/hal-00748607

C. Baudet, C. Lemaitre, Z. Dias, E. Tannier, C. Gautier et al., Cassis: detection of genomic rearrangement breakpoints, Bioinformatics, vol.26, issue.15, pp.1897-1898, 2010.
DOI : 10.1093/bioinformatics/btq301
URL : https://hal.archives-ouvertes.fr/hal-00681095

C. Baudet, C. Lemaitre, Z. Dias, E. Tannier, C. Gautier et al., Cassis: detection of genomic rearrangement breakpoints, Proceedings of the 9th European Conference on Computational Biology, p.25, 2010.
DOI : 10.1093/bioinformatics/btq301
URL : https://hal.archives-ouvertes.fr/hal-00681095

A. Bergeron, A very elementary presentation of the Hannenhalli???Pevzner theory, Discrete Applied Mathematics, vol.146, issue.2, pp.134-145, 2005.
DOI : 10.1016/j.dam.2004.04.010

A. Bergeron, C. Chauve, T. Hartman, and K. Saint-onge, On the properties of sequences of reversals that sort a signed permutation, Proceedings of the JOBIM 2002, pp.99-108, 2002.

A. Bergeron, S. Corteel, and M. Raffinot, The Algorithmic of Gene Teams, Proceedings of the Workshop on Algorithms in Bioinformatics, pp.464-476, 2002.
DOI : 10.1007/3-540-45784-4_36

A. Bergeron, J. Mixtacki, and J. Stoye, On Sorting by Translocations, Journal of Computational Biology, vol.13, issue.2, pp.567-578, 2006.
DOI : 10.1089/cmb.2006.13.567

P. Berman and S. Hannenhalli, Fast sorting by reversal, Proceedings of Combinatorial Pattern Matching (CPM'96), 7th Annual Symposium, pp.168-185, 1996.
DOI : 10.1007/3-540-61258-0_14

P. Berman, S. Hannenhalli, and M. Karpinski, 1.375-Approximation Algorithm for Sorting by Reversals, Proceedings of the 10th European Symposium on Algorithms (ESA'2002), 2002.
DOI : 10.1007/3-540-45749-6_21
URL : https://hal.archives-ouvertes.fr/in2p3-01192634

G. Blanc, H. Ogata, C. Robert, S. Audic, K. Suhre et al., Reductive Genome Evolution from the Mother of Rickettsia, PLoS Genetics, vol.44, issue.1, pp.103-114, 2007.
DOI : 10.1371/journal.pgen.0030014.st005

M. Blanchette, T. Kunisawa, and D. Sankoff, Parametric genome rearrangement, Gene, vol.172, issue.1, pp.11-17, 1996.
DOI : 10.1016/0378-1119(95)00878-0

G. Bourque, E. M. Zdobnov, P. Bork, P. A. Pevzner, and G. Tesler, Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages, Genome Research, vol.15, issue.1, pp.98-110, 2005.
DOI : 10.1101/gr.3002305

M. D. Braga, Exploring the Solution Space of Sorting by Reversals When Analyzing Genome Rearrangements, 2008.

M. D. Braga, baobabLUNA: the solution space of sorting by reversals, Bioinformatics, vol.25, issue.14, pp.1833-1835, 2009.
DOI : 10.1093/bioinformatics/btp285
URL : https://hal.archives-ouvertes.fr/hal-00539408

M. D. Braga, C. Gautier, and M. Sagot, An asymmetric approach to preserve common intervals while sorting by reversals, Algorithms for Molecular Biology, vol.4, issue.1, p.16, 2009.
DOI : 10.1186/1748-7188-4-16
URL : https://hal.archives-ouvertes.fr/hal-00784445

M. D. Braga, M. Sagot, C. Scornavacca, and E. Tannier, The Solution Space of Sorting by Reversals, Proceedings of the International Symposium on Bioinformatics Research and Applications, pp.293-304, 2007.
DOI : 10.1007/978-3-540-72031-7_27
URL : https://hal.archives-ouvertes.fr/hal-00434566

M. D. Braga, M. Sagot, C. Scornavacca, and E. Tannier, Exploring the Solution Space of Sorting by Reversals, with Experiments and an Application to Evolution, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.5, issue.3, pp.348-356, 2008.
DOI : 10.1109/TCBB.2008.16
URL : https://hal.archives-ouvertes.fr/hal-00428206

N. Bray, I. Dubchak, and L. Pachter, AVID: A Global Alignment Program, Genome Research, vol.13, issue.1, pp.97-102, 2003.
DOI : 10.1101/gr.789803

M. Brudno, M. Chapman, B. Göttgens, S. Batzoglou, and B. Morgenstern, Fast and sensitive multiple alignment of large genomic sequences, BMC Bioinformatics, vol.4, issue.66, p.11, 2003.

P. P. Calabrese, S. Chakravarty, and T. J. Vision, Fast identification and statistical evaluation of segmental homologies in comparative maps, Bioinformatics, vol.19, issue.Suppl 1, pp.74-80, 2003.
DOI : 10.1093/bioinformatics/btg1008

S. B. Cannon, A. Kozik, B. Chan, R. Michelmore, and N. D. Young, DiagHunter and GenoPix2D: programs for genomic comparisons, large-scale homology discovery and visualization, Genome Biology, vol.4, issue.10, p.68, 2003.
DOI : 10.1186/gb-2003-4-10-r68

A. Caprara, Sorting Permutations by Reversals and Eulerian Cycle Decompositions, SIAM Journal on Discrete Mathematics, vol.12, issue.1, pp.91-110, 1999.
DOI : 10.1137/S089548019731994X
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.55.7886

A. Caprara and G. Lancia, Experimental and statistical analysis of sorting by reversals Comparative Genomics: Empirical and Analyitical Approaches to Gene Order Dynamics, Map Alignment and Evolution of Gene Families, 2000.

P. Cartier and D. Foata, Probì emes combinatoires de commutation et réarrangements. Number 85 in Lecture Notes in Mathematics, 1969.
DOI : 10.1007/bfb0079468

V. Choi, C. Zheng, Q. Zhu, and D. Sankoff, Algorithms for the Extraction of Synteny Blocks from Comparative Maps, Proceedings of the Workshop on Algorithms in Bioinformatics, pp.277-288, 2007.
DOI : 10.1007/978-3-540-74126-8_26

D. A. Christie, Sorting permutations by block-interchanges, Information Processing Letters, vol.60, issue.4, pp.165-169, 1996.
DOI : 10.1016/S0020-0190(96)00155-X

D. A. Christie, A 3/2-approximation algorithm for sorting by reversals, Proceedings of the Ninth Annual ACM-SIAM Symposium on Discrete Algorithms, pp.244-252, 1998.

D. A. Christie, Genome Rearrangement Problems, 1998.

A. J. Clutterbuck and S. J. O-'brien, Genetics Maps: Locus Maps of Complex Genomes, 1993.

A. Coghlan, E. E. Eichler, S. G. Oliver, A. H. Paterson, and L. Stein, Chromosome evolution in eukaryotes: a multi-kingdom perspective, Trends in Genetics, vol.21, issue.12, pp.673-68273, 2003.
DOI : 10.1016/j.tig.2005.09.009

V. Curwen, E. Eyras, T. D. Andrews, L. Clarke, E. Mongin et al., The Ensembl Automatic Gene Annotation System, Genome Research, vol.14, issue.5, pp.942-950, 2004.
DOI : 10.1101/gr.1858004

E. Darai-ramqvist, A. Sandlund, S. Müller, G. Klein, S. Imreh et al., Segmental duplications and evolutionary plasticity at tumor chromosome break-prone regions, Genome Research, vol.18, issue.3, pp.370-379, 2008.
DOI : 10.1101/gr.7010208

A. C. Darling, B. Mau, F. R. Blattner, and N. T. Perna, Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements, Genome Research, vol.14, issue.7, pp.1394-1403, 2004.
DOI : 10.1101/gr.2289704

R. W. Debry and M. F. Seldin, Human/Mouse Homology Relationships, Genomics, vol.33, issue.3, pp.337-351, 1996.
DOI : 10.1006/geno.1996.0209

T. Derrien, C. André, F. Galibert, and C. Hitte, AutoGRAPH: an interactive web server for automating and visualizing comparative genome maps, Bioinformatics, vol.23, issue.4, pp.498-499, 2007.
DOI : 10.1093/bioinformatics/btl618

C. N. Dewey and L. Pachter, Evolution at the nucleotide level: the problem of multiple whole-genome alignment, Human Molecular Genetics, vol.15, issue.90001, pp.51-56, 2006.
DOI : 10.1093/hmg/ddl056

C. N. Dewey and L. Pachter, Mercator: Multiple whole-genome orthology map construction. webpage, 2006.

Z. Dias and J. Meidanis, Genome rearrangements distance by fusion, fission, and transposition is easy, Proceedings Eighth Symposium on String Processing and Information Retrieval, pp.250-253, 2001.
DOI : 10.1109/SPIRE.2001.989776

Y. Diekmann, M. Sagot, and E. Tannier, Evolution under Reversals: Parsimony and Conservation of Common Intervals, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.4, issue.2, pp.301-309, 2005.
DOI : 10.1109/TCBB.2007.1042
URL : https://hal.archives-ouvertes.fr/hal-00434588

T. Dobzhansky and A. H. Sturtevant, Inversions in the third chromosome of wild races of Drosophila pseudoobscura, and their use in the study of the history of the species, Proceedings of the National Academy of Science, vol.22, pp.448-450, 1936.

T. Dobzhansky and A. H. Sturtevant, Inversions in the chromosomes of Drosophila pseudoobscura, Genetics, vol.23, issue.1, p.28, 1938.

J. Dufayard, L. Duret, S. Penel, M. Gouy, F. Rechenmann et al., Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases, Bioinformatics, vol.21, issue.11, pp.2596-2603, 2005.
DOI : 10.1093/bioinformatics/bti325
URL : https://hal.archives-ouvertes.fr/hal-00427861

B. Dutrillaux, CommentévoluentCommentévoluent les chromosomes de mammifères, La Recherche, vol.296, pp.70-75, 1997.

R. C. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1797, 2004.
DOI : 10.1093/nar/gkh340

J. Ehrlich, D. Sankoff, and J. H. Nadeau, Synteny conservation and chromosome rearrangements during mammalian evolution, Genetics, vol.147, issue.1, pp.289-296, 1997.

J. A. Eisen, J. F. Heidelberg, O. White, and S. L. Salzberg, Evidence for symmetric chromosomal inversions around the replication origin in bacteria, Genome Biology, vol.19, issue.6, pp.11-12, 2000.

N. El-mabrouk and D. Sankoff, Genome rearrangement, Current Topics in Computational Biology, 2001.

I. Elias and T. Hartman, A 1.375-approximation algorithm for sorting by transpositions + ?)-approximation of sorting by reversals and transpositions, Proceedings of 5th Workshop on Algorithms in Bioinformatics (WABI'05, pp.204-215517, 2002.
URL : https://hal.archives-ouvertes.fr/hal-00662947

M. A. Ferguson-smith and V. Trifonov, Mammalian karyotype evolution, Nature Reviews Genetics, vol.55, issue.12, pp.950-962, 2007.
DOI : 10.1038/nrg2199

P. A. Fujita, B. Rhead, A. S. Zweig, A. S. Hinrichs, D. Karolchik et al., The UCSC Genome Browser database: update 2011, Nucleic Acids Research, vol.39, issue.Database, pp.1-7, 2010.
DOI : 10.1093/nar/gkq963

L. Gordon, S. Yang, M. Tran-gyamfi, D. Baggott, M. Christensen et al., Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions, Genome Research, vol.17, issue.11, pp.1603-1613, 2007.
DOI : 10.1101/gr.6775107

Q. Gu and K. Iwata, A heuristic algorithm for genome rearrangements, 1997.

Q. Gu, S. Peng, and H. Sudborough, A 2-approximation algorithm for genome rearrangements by reversals and transpositions, Theoretical Computer Science, vol.210, issue.2, pp.327-339, 1999.
DOI : 10.1016/S0304-3975(98)00092-9

B. J. Haas, A. L. Delcher, J. R. Wortman, and S. L. Salzberg, DAGchainer: a tool for mining segmental genome duplications and synteny, Bioinformatics, vol.20, issue.18, pp.3643-3646, 2004.
DOI : 10.1093/bioinformatics/bth397

S. Hampson, A. Mclysaght, B. Gaut, and P. Baldi, LineUp: Statistical Detection of Chromosomal Homology With Application to Plant Comparative Genomics, Genome Research, vol.13, issue.5, pp.999-1010, 2003.
DOI : 10.1101/gr.814403

S. Hannenhalli, Polynomial-time algorithm for computing translocation distance between genomes, Discrete Applied Mathematics, vol.71, issue.1-3, pp.137-151, 1996.
DOI : 10.1016/S0166-218X(96)00061-3

S. Hannenhalli, C. Chappey, E. V. Koonin, and P. A. Pevzner, Genome Sequence Comparison and Scenarios for Gene Rearrangements: A Test Case, Genomics, vol.30, issue.2, pp.299-311, 1995.
DOI : 10.1006/geno.1995.9873

S. Hannenhalli and P. A. Pevzner, Towards a computational theory of genome rearrangements, Lecture Notes in Computer Science, vol.1000, pp.184-200, 1995.
DOI : 10.1007/BFb0015244

S. Hannenhalli and P. A. Pevzner, Transforming men into mice (polynomial algorithm for genomic distance problem), Proceedings of IEEE 36th Annual Foundations of Computer Science, pp.581-592, 1995.
DOI : 10.1109/SFCS.1995.492588

S. Hannenhalli and P. A. Pevzner, To cut... or not to cut (applications of comparative physical maps in molecular evolution), Proceedings of the Seventh Annual ACM-SIAM Symposium on Discrete Algorithms, pp.304-313, 1996.

S. Hannenhalli and P. A. Pevzner, Transforming cabbage into turnip, Proceedings of the twenty-seventh annual ACM symposium on Theory of computing , STOC '95, pp.1-27, 1999.
DOI : 10.1145/225058.225112

R. S. Harris, Improved pairwise alignment of genomic DNA The Pennsylvania State Univeristy, 2007.

L. S. Heath and J. P. Vergara, Sorting by bounded block-moves, Discrete Applied Mathematics, vol.88, issue.1-3, pp.181-206, 1998.
DOI : 10.1016/S0166-218X(98)00072-9

L. S. Heath and J. P. Vergara, Sorting by short block-moves. Algorithmica, 2000.
DOI : 10.1007/s004530010041

S. Heber and J. Stoye, Finding All Common Intervals of k Permutations, Proceeding of the 12th Annual Symposium on Combinatorial Pattern Matching, pp.207-218, 2001.
DOI : 10.1007/3-540-48194-X_19

H. Hinsch, S. Hannenhalli, R. Hoberman, D. Sankoff, and D. Durand, Recurring genomic breaks in independent lineages support genomic fragility The statistical analysis of spatially clustered genes under the maximum gap criterion, BMC Evolutionary Biology, vol.6, issue.1, pp.90-121083, 2005.
DOI : 10.1186/1471-2148-6-90

T. J. Hubbard, B. L. Aken, S. Ayling, B. Ballester, K. Beal et al., Ensembl 2009, Nucleic Acids Research, vol.37, issue.Database, pp.690-697, 2009.
DOI : 10.1093/nar/gkn828
URL : http://doi.org/10.1093/nar/gkn828

T. J. Hubbard, B. L. Aken, K. Beal, B. Ballester, M. Caccamo et al., Ensembl 2007, Nucleic Acids Research, vol.35, issue.Database, pp.610-617, 2007.
DOI : 10.1093/nar/gkl996
URL : http://doi.org/10.1093/nar/gkl996

M. Jerrum, The complexity of finding minimum-length generator sequences, Theoretical Computer Science, vol.36, pp.265-289, 1985.
DOI : 10.1016/0304-3975(85)90047-7

H. Kaplan, R. Shamir, and R. E. Tarjan, A Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals, SIAM Journal on Computing, vol.29, issue.3, pp.880-892, 2000.
DOI : 10.1137/S0097539798334207

H. Kaplan and E. Verbin, Efficient Data Structures and a New Randomized Approach for Sorting Signed Permutations by Reversals, Proceeding of the 14th Annual Symposium on Combinatorial Pattern Matching, pp.170-185, 2003.
DOI : 10.1007/3-540-44888-8_13

J. D. Kececioglu and R. Ravi, Of mice and men: Algorithms for evolutionary distances between genomes with translocation, Proceedings of the 6th Annual Symposium on Discrete Algorithms, pp.604-613, 1995.

J. D. Kececioglu and D. Sankoff, Exact and approximation algorithms for sorting by reversals, with application to genome rearrangement, Algorithmica, vol.84, issue.4, pp.180-210, 1995.
DOI : 10.1007/BF01188586

H. Kehrer-sawatzki and D. N. Cooper, Molecular mechanisms of chromosomal rearrangement during primate evolution, Chromosome Research, vol.14, issue.1, pp.41-56, 2008.
DOI : 10.1007/s10577-007-1207-1

J. W. Kent, BLAT---The BLAST-Like Alignment Tool, Genome Research, vol.12, issue.4, pp.656-664, 2002.
DOI : 10.1101/gr.229202

W. J. Kent, R. Baertsch, A. Hinrichs, W. Miller, and D. Haussler, Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes, Proceedings of the National Academy of Sciences, pp.10011484-11489, 2003.
DOI : 10.1073/pnas.1932072100

W. J. Kent, C. W. Sugnet, T. S. Furey, K. M. Roskin, T. H. Pringle et al., The Human Genome Browser at UCSC, Genome Research, vol.12, issue.6, pp.996-1006, 2002.
DOI : 10.1101/gr.229102

L. Klasson, T. Walker, M. Sebaihia, M. J. Sanders, M. A. Quail et al., Genome Evolution of Wolbachia Strain wPip from the Culex pipiens Group, Molecular Biology and Evolution, vol.25, issue.9, pp.1877-1887, 2008.
DOI : 10.1093/molbev/msn133

J. O. Korbel, A. E. Urban, J. P. Affourtit, B. Godwin, F. Grubert et al., Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome, Science, vol.318, issue.5849, pp.318420-426, 2007.
DOI : 10.1126/science.1149504

B. T. Lahn and D. C. Page, Four Evolutionary Strata on the Human X Chromosome, Science, vol.286, issue.5441, pp.964-967, 1999.
DOI : 10.1126/science.286.5441.964

C. Ledergerber and C. Dessimoz, Alignments with non-overlapping moves, inversions and tandem duplications in O(n 4) time, Journal of Combinatorial Optimization, vol.61, issue.3, pp.263-278, 2007.
DOI : 10.1007/s10878-007-9132-y

C. Lemaitre and M. Sagot, A small trip in the untranquil world of genomes, Theoretical Computer Science, vol.395, issue.2-3, pp.171-192, 2008.
DOI : 10.1016/j.tcs.2008.01.014
URL : https://hal.archives-ouvertes.fr/hal-00428176

C. Lemaitre, E. Tannier, C. Gautier, and M. Sagot, Precise detection of rearrangement breakpoints in mammalian chromosomes, BMC Bioinformatics, vol.9, issue.1, p.286, 2008.
DOI : 10.1186/1471-2105-9-286
URL : https://hal.archives-ouvertes.fr/inria-00278553

G. Li, X. Qi, X. Wang, and B. Zhu, Combinatorial Pattern Matching, volume 3109 of Lecture Notes in Computer Science, chapter A Linear-Time Algorithm for Computing Translocation Distance between Signed Genomes, pp.323-332, 2004.

H. Li, Softwares for Phylogenetic Trees, 2010.

L. Li, C. J. Stoeckert, and D. S. Roos, OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes, Genome Research, vol.13, issue.9, pp.2178-2189, 2003.
DOI : 10.1101/gr.1224503

Z. Li and L. Wang, Algorithmic approaches for genome rearrangement: A review, IEEE Transactions on Systems, Man, and Cybernetics, vol.36, issue.5, pp.636-648, 2006.

G. Lin and G. Xue, Signed genome rearrangement by reversals and transpositions: Models and approximations, Fifth Annual International Computing and Combinatorics Conference (COCOON'99), pp.71-80, 1999.
DOI : 10.1007/3-540-48686-0_7
URL : http://dx.doi.org/10.1016/s0304-3975(00)00038-4

B. Ma, J. Tromp, and M. Li, PatternHunter: faster and more sensitive homology search, Bioinformatics, vol.18, issue.3, pp.440-445, 2002.
DOI : 10.1093/bioinformatics/18.3.440
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.147.8001

J. Ma, L. Zhang, B. B. Suh, B. J. Raney, R. C. Burhans et al., Reconstructing contiguous regions of an ancestral genome, Genome Research, vol.16, issue.12, pp.1557-1565, 2006.
DOI : 10.1101/gr.5383506

P. Mackiewicz, D. Mackiewicz, M. Kowalczuk, and S. Cebrat, Flip-flop around the origin and terminus of replication in prokariotic genomes, Genome Biology, vol.2, issue.12, pp.1004-1005, 2001.

J. Meidanis, M. E. Walter, and Z. Dias, A Lower Bound on the Reversal and Transposition Diameter, Journal of Computational Biology, vol.9, issue.5, 2000.
DOI : 10.1089/106652702761034163

W. J. Murphy, D. M. Larkin, A. E. Van-der-wind, G. Bourque, G. Tesler et al., Dynamics of Mammalian Chromosome Evolution Inferred from Multispecies Comparative Maps, Science, vol.309, issue.5734, pp.309613-617, 2005.
DOI : 10.1126/science.1111387

J. H. Nadeau and D. Sankoff, The lengths of undiscovered conserved segments in comparative maps, Mammalian Genome, vol.9, issue.6, pp.491-495, 1998.
DOI : 10.1007/s003359900806

J. H. Nadeau and B. A. Taylor, Lengths of chromosomal segments conserved since divergence of man and mouse., Proceedings of the National Academy Science, pp.814-818, 1984.
DOI : 10.1073/pnas.81.3.814

T. L. Newman, E. Tuzun, V. A. Morrison, K. E. Hayden, M. Ventura et al., A genome-wide survey of structural variation between human and chimpanzee, Genome Research, vol.15, issue.10, pp.151344-1356, 2005.
DOI : 10.1101/gr.4338005

R. A. Notebaart, M. A. Huynen, B. Teusink, R. J. Siezen, B. Snel et al., Correlation between sequence conservation and the genomic context after gene duplication, Nucleic Acids Research, vol.33, issue.19, pp.6164-6171, 2005.
DOI : 10.1093/nar/gki913

S. Ohno, Sex chromosomes and sex-linked genes, 1967.

R. D. Page and M. A. Charleston, From Gene to Organismal Phylogeny: Reconciled Trees and the Gene Tree/Species Tree Problem, Molecular Phylogenetics and Evolution, vol.7, issue.2, pp.231-240, 1997.
DOI : 10.1006/mpev.1996.0390

J. D. Palmer and L. A. Herbon, Plant mitochondrial DNA evolves rapidly in structure, but slowly in sequence, Journal of Molecular Evolution, vol.27, pp.87-97, 1988.

X. Pan, L. Stein, and V. Brendel, SynBrowse: a synteny browser for comparative sequence analysis, Bioinformatics, vol.21, issue.17, pp.3461-3468, 2005.
DOI : 10.1093/bioinformatics/bti555

E. Passarge, B. Horsthemke, and R. A. Farber, Incorrect use of the term synteny, Nature Genetics, vol.23, issue.4, p.387, 1999.
DOI : 10.1038/70486

G. Pavesi, G. Mauri, F. Iannelli, C. Gissi, and G. Pesole, GeneSyn: a tool for detecting conserved gene order across genomes, Bioinformatics, vol.20, issue.9, pp.1472-1474, 2004.
DOI : 10.1093/bioinformatics/bth102

Q. Peng, P. A. Pevzner, and G. Tesler, The Fragile Breakage versus Random Breakage Models of Chromosome Evolution, PLoS Computational Biology, vol.65, issue.2, p.14, 2006.
DOI : 10.1371/journal.pcbi.0020014.sg002

P. Peterlongo, Filtrage de séquences d'ADN pour la recherche de longues répétitions multiples, 2006.

P. Peterlongo, N. Pisanti, F. Boyer, A. Pereira, M. Lago et al., Lossless filter for multiple repetitions with Hamming distance, Journal of Discrete Algorithms, vol.6, issue.3, pp.497-509, 2008.
DOI : 10.1016/j.jda.2007.03.003
URL : https://hal.archives-ouvertes.fr/inria-00179731

P. Peterlongo, G. A. Sacomoto, A. Pereira-do-lago, N. Pisanti, and M. Sagot, Lossless filter for multiple repeats with bounded edit distance, Algorithms for Molecular Biology, vol.4, issue.1, 2009.
DOI : 10.1186/1748-7188-4-3
URL : https://hal.archives-ouvertes.fr/hal-00784457

P. A. Pevzner, Computational Molecular Biology: An Algorithmic Approach, 2000.

P. A. Pevzner and G. Tesler, Genome Rearrangements in Mammalian Evolution: Lessons From Human and Mouse Genomes, Genome Research, vol.13, issue.1, pp.37-45, 2003.
DOI : 10.1101/gr.757503

P. A. Pevzner and G. Tesler, Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution, Proceedings of the National Academy of Sciences, pp.1007672-7677, 2003.
DOI : 10.1073/pnas.1330369100

S. C. Potter, L. Clarke, V. Curwen, S. Keenan, E. Mongin et al., The Ensembl Analysis Pipeline, Genome Research, vol.14, issue.5, pp.934-941, 2004.
DOI : 10.1101/gr.1859804

K. D. Pruitt, J. Harrow, R. A. Harte, C. Wallin, M. Diekhans et al., The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes, Genome Research, vol.19, issue.7, pp.1316-1323, 2009.
DOI : 10.1101/gr.080531.108

D. Rasko, G. Myers, and J. , Visualization of comparative genomic analyses by BLAST score ratio, BMC Bioinformatics, vol.6, issue.12, 2005.

. Ricbase, Rickettsia genome database, 2009.

M. T. Ross, The DNA sequence of the human X chromosome, Nature, vol.428, issue.7031, pp.325-337, 2005.
DOI : 10.1093/hmg/9.2.311

]. D. Sankoff, Edit distance for genome comparison based on non-local operations, Proceedings of the Third Annual Symposium of the Combinatorial Pattern Matching (CPM'92), number 664 in Lecture Notes in Computer Science, pp.121-135, 1992.
DOI : 10.1007/3-540-56024-6_10

D. Sankoff, The Signal in the Genomes, PLoS Computational Biology, vol.13, issue.4, p.35, 2006.
DOI : 1066-5277(2006)013[0554:SORMIT]2.0.CO;2

D. Sankoff, G. Leduc, N. Antoine, B. Paquin, B. F. Lang et al., Gene order comparisons for phylogenetic inference: evolution of the mitochondrial genome., Proceedings of the National Academy Science, pp.6575-6579, 1992.
DOI : 10.1073/pnas.89.14.6575

D. Sankoff and J. H. Nadeau, Chromosome rearrangements in evolution: From gene order to genome sequence and back, Proceedings of the National Academy of Sciences, pp.10011188-11189, 2003.
DOI : 10.1073/pnas.2035002100

D. Sankoff and P. Trinh, Chromosomal Breakpoint Reuse in Genome Sequence Rearrangement, Journal of Computational Biology, vol.12, issue.6, pp.812-821, 2005.
DOI : 10.1089/cmb.2005.12.812

S. Schwartz, W. J. Kent, A. Smit, Z. Zhang, R. Baertsch et al., Human-Mouse Alignments with BLASTZ, Genome Research, vol.13, issue.1, pp.103-107, 2003.
DOI : 10.1101/gr.809403
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961

A. C. Siepel, An algorithm to enumerate all sorting reversals, Proceedings of the sixth annual international conference on Computational biology , RECOMB '02, pp.575-597, 2003.
DOI : 10.1145/565196.565233

A. U. Sinha and J. Meller, Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms, BMC Bioinformatics, vol.8, issue.1, p.82, 2007.
DOI : 10.1186/1471-2105-8-82

H. Skaletsky, The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes, Nature, vol.423, issue.6942, pp.825-837, 2003.
DOI : 10.1038/nature01722

D. Smedley, S. Haider, B. Ballester, R. Holland, D. London et al., BioMart ??? biological queries made easy, BMC Genomics, vol.10, issue.1, 2009.
DOI : 10.1186/1471-2164-10-22

Y. Sun and J. Buhler, Choosing the best heuristic for seeded alignment of DNA sequences, BMC Bioinformatics, vol.7, issue.1, p.133, 2006.
DOI : 10.1186/1471-2105-7-133

K. M. Swenson, G. Badr, and D. Sankoff, Listing all sorting reversals in quadratic time, Proceedings of the 10th Workshop in Algorithms in Bioinformatics, 2010.
DOI : 10.1089/cmb.2006.13.1005

K. M. Swenson, Y. Lin, V. Rajan, and B. M. Moret, Hurdles Hardly Have to Be Heeded, Proceedings of the International Workshop on Comparative Genomics (RECOMB-CG'08), pp.241-251, 2008.
DOI : 10.1007/978-3-540-87989-3_18

K. M. Swenson, V. Rajan, Y. Lin, and B. M. Moret, ) Time, Journal of Computational Biology, vol.17, issue.3, pp.489-501, 2010.
DOI : 10.1089/cmb.2009.0184

F. Swidan, E. P. Rocha, M. Shmoish, and R. Y. Pinter, An integrative method for accurate comparative genome mapping, PLoS Computational Biology, vol.2, issue.8, 2006.

E. Tannier, A. Bergeron, and M. Sagot, Advances on sorting by reversals, Discrete Applied Mathematics, vol.155, issue.6-7, pp.881-888, 2007.
DOI : 10.1016/j.dam.2005.02.033
URL : https://hal.archives-ouvertes.fr/hal-00434657

R. L. Tatusov, E. V. Koonin, and D. J. Lipman, A Genomic Perspective on Protein Families, Science, vol.278, issue.5338, pp.631-637, 1997.
DOI : 10.1126/science.278.5338.631

P. Trinh, A. Mclysaght, and D. Sankoff, Genomic features in the breakpoint regions between syntenic blocks, Bioinformatics, vol.20, issue.Suppl 1, pp.318-325, 2004.
DOI : 10.1093/bioinformatics/bth934

A. E. Van-der-wind, S. R. Kata, M. R. Band, M. Rebeiz, D. M. Larkin et al., A 1463 gene cattle-human comparative map with anchor points defined by human genome sequence coordinates The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice, Genome Research Genome Research, vol.14160, issue.1211, pp.1424-14371792, 2002.

A. F. Vellozo, C. E. Alves, and A. P. Lago, Alignment with Non-overlapping Inversions in O(n 3)-Time, Algorithms in Bioinformatics Proceedings of the WABI, pp.186-196, 2006.
DOI : 10.1007/11851561_18

A. J. Vilella, J. Severing, A. Ureta-vidal, L. Heng, R. Durbin et al., EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates, Genome Research, vol.19, issue.2, pp.327-335, 2009.
DOI : 10.1101/gr.073585.107

M. E. Walter, Z. Dias, and J. Meidanis, Reversal and transposition distance of linear chromosomes, Proceedings. String Processing and Information Retrieval: A South American Symposium (Cat. No.98EX207), 1998.
DOI : 10.1109/SPIRE.1998.712988

M. E. Walter, Z. Dias, and J. Meidanis, A new approach for approximating the transposition distance, Proceedings Seventh International Symposium on String Processing and Information Retrieval. SPIRE 2000, 2000.
DOI : 10.1109/SPIRE.2000.878196

L. Wang, D. Zhu, X. Liu, and S. Ma, An <mml:math altimg="si1.gif" overflow="scroll" xmlns:xocs="http://www.elsevier.com/xml/xocs/dtd" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://www.elsevier.com/xml/ja/dtd" xmlns:ja="http://www.elsevier.com/xml/ja/dtd" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:tb="http://www.elsevier.com/xml/common/table/dtd" xmlns:sb="http://www.elsevier.com/xml/common/struct-bib/dtd" xmlns:ce="http://www.elsevier.com/xml/common/dtd" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:cals="http://www.elsevier.com/xml/common/cals/dtd"><mml:mi>O</mml:mi><mml:mo stretchy="false">(</mml:mo><mml:msup><mml:mrow><mml:mi>n</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msup><mml:mo stretchy="false">)</mml:mo></mml:math> algorithm for signed translocation, Journal of Computer and System Sciences, vol.70, issue.3, pp.284-299, 2005.
DOI : 10.1016/j.jcss.2004.12.005

L. Wang, Exact-IEBP: A New Technique for Estimating Evolutionary Distances between Whole Genomes, Lecture Notes in Computer Science, vol.2149, pp.175-188, 2001.
DOI : 10.1007/3-540-44696-6_14

L. Wang and T. Warnow, Estimating true evolutionary distances between genomes, Proceedings of the thirty-third annual ACM symposium on Theory of computing , STOC '01, pp.637-646, 2001.
DOI : 10.1145/380752.380861

R. H. Waterston, K. Lindblad-toh, E. Birney, J. Rogers, J. F. Abril et al., Initial sequencing and comparative analysis of the mouse genome, Nature, issue.6915, pp.420520-562, 2002.

L. G. Wilming, G. R. Gilbert, K. Howe, S. Trevanion, T. Hubbard et al., The vertebrate genome annotation (Vega) database, Nucleic Acids Research, vol.36, issue.Database, pp.753-760, 2008.
DOI : 10.1093/nar/gkm987

Y. Yue, B. Grossmann, M. Ferguson-smith, T. Yang, and . Haaf, Comparative cytogenetics of human chromosome 3q21.3 reveals a hot spot for ectopic recombination in hominoid evolution, Genomics, vol.85, issue.1, pp.36-47, 2005.
DOI : 10.1016/j.ygeno.2004.10.007

J. J. Yunis, J. R. Sawyer, and K. Dunham, The striking resemblance of high-resolution G-banded chromosomes of man and chimpanzee, Science, vol.208, issue.4448, pp.1145-1148, 1980.
DOI : 10.1126/science.7375922

E. M. Zdobnov, C. Von-mering, I. Letunic, D. Torrents, M. Suyama et al., Comparative Genome and Proteome Analysis of Anopheles gambiae and Drosophila melanogaster, Science, vol.298, issue.5591, pp.298149-159, 2002.
DOI : 10.1126/science.1077061

Z. Zhang, B. Raghavachari, R. C. Hardison, and W. Miller, Chaining Multiple-Alignment Blocks, Journal of Computational Biology, vol.1, issue.3, pp.217-226, 1994.
DOI : 10.1089/cmb.1994.1.217

C. Zheng and D. Sankoff, Rearrangement of Noisy Genomes, Proceedings of the International Conference on Computational Science, pp.791-798, 2006.
DOI : 10.1007/11758525_106

D. M. Zhu and S. H. Ma, Improved polynomial-time algorithm for computing translocation distance between genomes, Chinese, pp.189-196, 2002.