Perfect sorting by reversals is not always difficult

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 3692 LNBI, Issue , 2005, Pages 228-238

  Bérard, Sèverine ^a   Bergeron, Anne ^b   Chauve, Cedric ^b   Paul, Christophe ^c  

^a CEMAGREF   (France)

^b UNIVERSITÉ DU QUÉBEC À MONTRÉAL   (Canada)

^c LIRMM   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; CHROMOSOMES; COMPUTATION THEORY; COMPUTATIONAL COMPLEXITY; POLYNOMIALS; PROBLEM SOLVING; QUADRATIC PROGRAMMING; TIME DOMAIN ANALYSIS;

COMBINATORIAL STRUCTURES; PARSIMONIOUS; PERMUTATIONS; PIGEAC AND VARRE;

COMBINATORIAL MATHEMATICS;

EID: 33646200543     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/11557067_19     Document Type: Conference Paper

References (22)

1. D. A. Bader, B. M. E. Moret and M. Yan. A linear-time algorithm for computing inversion distance between signed permutations with an experimental study. J. Comp. Biol., 8(5):483-491, 2001.
2. S. Bérafd, A. Bergeron and C. Chauve. Conserved structures in evolution scenarios. In RCG 2004, volume 3388 of Lecture Notes in Bioinformatics, p. 1-15, 2005.
3. S. Bérard, A. Bergeron, C. Chauve and C. Paul. Perfect sorting by reversals is not always difficult. Technical Report LIRMM RR-05042 (Montpllier, France), 2005.
4. A. Rergeron, M. Blanchette, A. Chateau nnrt C. Chauve Reconstructing ancestral gene orders using conserved intervals. In WABI 2004, Volume 3240 of Lecture Notes in Bioinformatics, p. 14-25, 2004.
5. A. Bergeron, C. Chauve, T. Hartman and K. St-Onge. On the properties of sequences of reversals that sort a signed permutation. In JOBIM 2002, p. 99-108, 2002.
6. A. Bergeron, C. Chauve, F. de Montgolfier and M. Raffinot. Computing common intervls of K permutations, with applications to modular decomposition of graphs. To appear in ESA 2005, (to be published in Lecture Notes in Comput. Sci.), 2005.
7. A. Bergeron, J. Mixtacki. and J. Stoye. Reversal distance without hurdles and fortresses. In CPM 2004, volume 3109 of Lecture Notes in Comput. Sci., p. 388-399, 2004.
8. G. Bourque and P. A. Pevzner. Genome-scale evolution: Reconstructing gene orders in the ancestral species. Genome Res., 12(1):26-36, 2002.
9. G. Bourque, P. A. Pevzner and G. Tesler. Reconstructing the genomic architecture of ancestral mammals: Lessons from human, mouse, and rat genomes. Genome Res., 14(4):507-516, 2004.
10. A. Caprara. Formulations and hardness of multiple sorting by reversals. In RECOMB'99, p. 84-94, ACM Press, 1999.
11. M. Chein, M. Habib and M. C. Maurer. Partitive hypergraphs. Discrete Math., 37(1):35-50, 1981.
12. G. Didier. Common intervals of two sequences. In WABI 2003, volume 2812 of Lecture Notes in Bioinformatics, p. 17-24, 2003.
13. M. Figeac and J.-S. Varré. Sorting by reversals with common intervals. In WABI 2004, volume 3240 of Lecture Notes in Bio-Informatics, p. 26-37, 2004.
14. R. A. Gibbs et al. Genome sequence of the brown norway rat yields insights into mammalian evolution. Nature, 428(6982);493-521, 2004.
15. S. Heber and J. Stoye. Finding all common intervals of k permutations. In CPM 2001, volume 2089 of Lecture Notes in Comput. Sci., p. 207-218, 2001.
16. G.M. Landau, L. Parida and O. Weimann. Using PQ trees for comparative genomics. In CPM 2005, volume 3537 of Lecture Notes in Comput. Sci., p. 128-143, 2005.
17. F. de Montgolfier Decomposition modulaire des graphes. Théorie, extensions et algorithmes. Ph.D. thesis, Université Montpellier II (France), 2003.
18. M.-F. Sagot and E. Tannier. Perfect sorting by reversals. In COCOON 2005, volume 3595 of Lecture Notes in Comput. Sci., pages 42-52, 2005.
19. D. Sankoff. Edit distance for genome comparison based on non-local operations. In CPM 1992, volume 644 of Lecture Notes in Comput. Sci., p. 121-135, 1992.
20. T. Schmidt and J. Stoye. Quadratic time algorithms for finding common intervals in two and more sequences. In CPM 2004, volume 3109 of Lecture Notes in Comput, Sci., p. 347-358, 2004.
21. E. Tannier and M.-F. Sagot. Sorting by reversals in subquadratic time. In CPM 2004, volume 3109 of Lecture Notes in Comput. Sci., p. 1-13, 2004.
22. T. Uno and M. Yagiura. Fast, algorithms to enumerate all common intervals of two permutations. Algorithmica, 26(2):290-309, 2000.