The median problem for the reversal distance in circular bacterial genomes

Lecture Notes in Computer Science

Volumn 3537, Issue , 2005, Pages 116-127

  Ohlebusch, Enno ^a   Abouelhoda, Mohamed Ibrahim ^a   Hockel, Kathrin ^a   Stallkamp, Jan ^a  

^a UNIVERSITY OF ULM   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; GENES; PROBLEM SOLVING;

BACTERIAL GENES; GENOME REARRANGEMENT; PHYLOGENETIC TREE; REVERSAL DISTANCE;

PATTERN MATCHING;

EID: 26444512111     PISSN: 03029743     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1007/11496656_11     Document Type: Conference Paper

References (19)

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. Journal of Computational Biology, 8:483-491, 2001.
2. A. Bergeron, J. Mixtacki, and J. Stoye. Reversal distance without hurdles and fortresses. In Proc. 15th Annual Symposium on Combinatorial Pattern Matching, volume 3109 of Lecture Notes in Computer Science, pages 388-399. Springer-Verlag, 2004.
3. M. Blanchette, G. Bourque, and D. Sankoff. Breakpoint phylogenies. In Proc. Genome Informatics Workshop, pages 25-34. Univ. Academy Press, 1997.
4. B. Bourque and P.A. Pevzner. Genome-scale evolution: Reconstructing gene orders in the ancestral species. Genome Research, 12(1):26-36, 2002.
5. A. Caprara. Formulations and hardness of multiple sorting by reversals. In Proc. 3rd Annual International Conference on Research in Computational Molecular Biology, pages 84-94. ACM Press, 1999.
6. A. Caprara. On the practical solution of the reversal median problem. In Proc. 1st International Workshop on Algorithms in Bioinformatics, volume 2149 of Lecture Notes in Computer Science, pages 238-251. Springer-Verlag, 2001.
7. T. Dobzhansky and A.H. Sturtevant. Inversions in the chromosomes of Drosophila pseudoobscura. Genetics, 23:28-64, 1938.
8. 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, 1(6): 1-9, 2000.
9. S. Hannenhalli and P.A. Pevzner. Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals). Journal of the ACM, 48:1-27, 1999.
10. D. Hughes. Evaluating genome dynamics: The constraints on rearrangements within bacterial genomes. Genome Biology, 1(6): 1-8, 2000.
11. H. Kaplan, R. Shamir, and R.E. Tarjan. A faster and simpler algorithm for sorting signed permutations by reversals. SIAM J. Comput., 29(3):880-892, 1999.
12. B.M.E. Moret, A.C. Siepel, J. Tang, and T. Liu. Inversion medians outperform breakpoint medians in phylogeny reconstruction from gene-order data. In Proc. 2nd International Workshop on Algorithms in Bioinformatics, volume 2542 of Lecture Notes in Computer Science, pages 521-536. Springer-Verlag, 2002.
13. J.H. Nadeau and B.A. Taylor. Lengths of chromosomal segments conserved since divergence of man and mouse. Proceedings of the National Academy of Sciences of the United States of America, 81(3):814-818, 1984.
14. I. Pe'er and R. Shamir. The median problems for breakpoints are NP-complete. Technical Report TR98-071, Electronic Colloquium on Computational Complexity, 1998.
15. D. Sankoff. Edit distance for genome comparison based on non-local operations. In Proc. 3rd Annual Symposium on Combinatorial Pattern Matching, 3rd Annual Symposium, volume 644 of Lecture Notes in Computer Science, pages 121-135. Springer-Verlag, 1992.
16. D. Sankoff and M. Blanchette. Multiple genome rearrangement and breakpoint phylogeny. Journal of Computational Biology, 5(3):555-570, 1998.
17. A.C. Siepel and B.M.E. Moret. Finding an optimal inversion median: Experimental results. In Proc. 1st International Workshop on Algorithms in Bioinformatics, volume 2149 of Lecture Notes in Computer Science, pages 189-203. Springer-Verlag, 2001.
18. E.R.M. Tiller and R. Collins. Genome rearrangement by replication-directed translocation. Nature Genetics, 26:195-197, 2000.
19. G.A. Watterson, W.J. Ewens, T.E. Hall, and A. Morgan. The chromosome inversion problem. Journal of Theoretical Biology, 99:1-7, 1982.