Finding an optimal inversion median: Experimental results

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

Volumn 2149, Issue , 2001, Pages 189-203

  Siepel, Adam C ^a,b   Moret, Bernard M E ^a  

^a University of New Mexico   (United States)

^b NATIONAL CENTER FOR GENOME RESOURCES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; BIOLOGY; BRANCH AND BOUND METHOD; FORESTRY; TREES (MATHEMATICS);

BRANCH-AND-BOUND ALGORITHMS; GEOMETRIC PROPERTIES; INVERSION DISTANCE; LINEAR TIME; PHYLOGENY RECONSTRUCTION; SEARCH TREES; SIGNED PERMUTATIONS; SIMULATED DATASETS;

ALGORITHMS;

EID: 84959066123     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/3-540-44696-6_15     Document Type: Conference Paper

References (23)

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. In Proceedings 7th Workshop on Algorithms and Data Structures WADS 91. Springer Verlag, 2001. to appear in LNCS.
2. P. Berman and S. Hannenhalli. Fast sorting by reversal. In D. Hirschberg and E. Myers, editors, Proceedings of the 7th Annual Symposium on Combinatorial Pattern Matching, pages 168–185, 1996.
3. M. Blanchette, T. Kunisawa, and D. Sankoff. Parametric genome rearrangement. Gene, 172:GC11–GC17, 1996.
4. A. Caprara. Formulations and complexity of multiple sorting by reversals. In S. Istrail, P.A. Pevzner, and M.S. Waterman, editors, Proceedings of the Third Annual International Conference on Computational Molecular Biology (RECOMB-99), pages 84–93, Lyon, France, April 1999.
5. M.E. Cosner, R.K. Jansen, B.M.E. Moret, L.A. Raubeson, L.-S. Wang, T. Warnow, and S. Wyman. An empirical comparison of phylogenetic methods on chloroplast gene order data in Campanulaceae. In D. Sankoff and J.H. Nadeau, editors, Comparative Genomics, pages 99–122. Kluwer Academic Press, 2000.
6. M.E. Cosner, R.K. Jansen, B.M.E. Moret, L.A. Raubeson, L.-S. Wang, T. Warnow, and S. Wyman. A new fast heuristic for computing the breakpoint phylogeny and experimental phylogenetic analyses of real and synthetic data. In Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology ISMB-2000, pages 104–115, 2000.
7. T. Dobzhansky and A.H. Sturtevant. Inversions in the chromosomes of Drosophila pseudoobscura. Genetics, 23:28–64, 1938.
8. D.S. Goldberg, S. McCouch, and J. Kleinberg. Algorithms for constructing comparative maps. In D. Sankoff and J.H. Nadeau, editors, Comparative Genomics. Kluwer Academic Press, 2000.
9. S. Hannenhalli, C. Chappey, E.V. Koonin, and P.A. Pevzner. Genome sequence comparison and scenarios for gene rearrangements: A test case. Genomics, 30:299–311, 1995.
10. S. Hannenhalli and P.A. Pevzner. Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals). In Proceedings of the 27th Annual ACM Symposium on the Theory of Computing, pages 178–189, 1995.
11. S. Hannenhalli and P.A. Pevzner. Transforming men into mice (polynomial algorithm for genomic distance problem). In Proceedings of the 36th Annual IEEE Symposium on Foundations of Computer Science, pages 581–592, 1995.
12. H. Kaplan, R. Shamir, and R.E. Tarjan. A faster and simpler algorithm for sorting signed permutations by reversals. SIAM Journal of Computing, 29(3):880–892, 1999.
13. A. McLysaght, C. Seoighe, and K.H. Wolfe. High frequency of inversions during eukaryote gene order evolution. In D. Sankoff and J.H. Nadeau, editors, Comparative Genomics, pages 47–58. Kluwer Academic Press, 2000.
14. B.M.E. Moret, D.A. Bader, S. Wyman, T. Warnow, and M. Yan. A new implementation and detailed study of breakpoint analysis. In R.B. Altman, A.K. Dunker, L. Hunter, K. Lauderdale, and T.E. Klein, editors, Pacific Symposium on Biocomputing 2001, pages 583–594. World Scientific Publ. Co., 2001.
15. B.M.E. Moret, L.-S. Wang, T. Warnow, and S.K. Wyman. New approaches for reconstructing phylogenies from gene-order data. In Proceedings 9th International Conference on Intelligent Systems for Molecular Biology ISMB-2001, 2001. to appear in Bioinformatics.
16. Pavel A. Pevzner. Computational Molecular Biology: An Algorithmic Approach. MIT Press, 2000.
17. D. Sankoff and M. Blanchette. Multiple genome rearrangement and breakpoint phylogeny. Journal of Computational Biology, 5(3):555–570, 1998.
18. D. Sankoff, D. Bryant, M. Deneault, B.F. Lang, and G. Burger. Early eukaryote evolution based on mitochondrial gene order breakpoints. Journal of Computational Biology, 7(3/4):521–535, 2000.
19. D. Sankoff and N. El-Mabrouk. Genome rearrangement. In T. Jiang, Y. Xu, and M. Zhang, editors, Topics in Computational Biology. MIT Press, 2001.
20. D. Sankoff, V. Ferretti, and J.H. Nadeau. Conserved segment identification. Journal of Computational Biology, 4(4):559–565, 1997.
21. D. Sankoff, G. Leduc, N. Antoine, B. Paquin, and B.F. Lang: Gene order comparisons for phylogenetic inference: Evolution of the mitochondrial genome. Proceedings of the National Academy of Sciences, 89:6575–6579, 1992.
22. J. Setubal and J. Meidanis. Introduction to Computational Molecular Biology. PWS Publishing, 1997.
23. G.A. Watterson, W.J. Ewens, and T.E. Hall. The chromosome inversion problem. Journal of Theoretical Biology, 99:1–7, 1982.