Sorting signed permutations by inversions in O(nlogn) time

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

Volumn 5541 LNBI, Issue , 2009, Pages 386-399

  Swenson, Krister M ^a   Rajan, Vaibhav ^a   Lin, Yu ^a   Moret, Bernard M E ^a  

^a EPFL   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

DETERMINISTIC ALGORITHMS; GENOMICS; IMPROVED ALGORITHM; INVERSION DISTANCE; LINEAR-TIME ALGORITHMS; POLYNOMIAL-TIME ALGORITHMS; RANDOMIZED ALGORITHMS; SIGNED PERMUTATIONS; SORTING ALGORITHM; STANDARD DEVIATION; SUBQUADRATIC ALGORITHMS;

BIOCHEMISTRY; CLUSTERING ALGORITHMS; MOLECULAR BIOLOGY; MOLECULAR STRUCTURE; SORTING;

COMPUTATION THEORY;

EID: 67650330340     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-02008-7_28     Document Type: Conference Paper

References (17)

1. Bader, D.A., Moret, B.M.E., Yan, M.: A fast linear-time algorithm for inversion distance with an experimental comparison. J. Comput. Biol. 8(5), 483-491 (2001)
2. Bergeron, A., Heber, S., Stoye, J.: Common intervals and sorting by reversals: a marriage of necessity. In: Proc. 2nd European Conf. Comput. Biol. ECCB 2002, pp. 54-63 (2002)
3. Bergeron, A., Stoye, J.: On the similarity of sets of permutations and its applications to genome comparison. In: Warnow, T.J., Zhu, B. (eds.) COCOON 2003. LNCS, vol. 2697, pp.68-79. Springer, Heidelberg (2003)
4. Caprara, A.: Sorting by reversals is difficult. In: Proc. 1st Int'l Conf. Comput. Mol. Biol. (RECOMB 1997), pp. 75-83 (1997)
5. Day,W.H.E., Sankoff, D.: The computational complexity of inferring phylogenies from chromosome inversion data. J. Theor. Biol. 127, 213-218 (1987)
6. Hannenhalli, S., Pevzner, P.A.: Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals). In: Proc. 27th Ann. ACM Symp. Theory of Comput (STOC 1995), pp. 178-189. ACM Press, New York (1995)
7. Kaplan, H., Verbin, E.: Efficient data structures and a new randomized approach for sorting signed permutations by reversals. In: Baeza-Yates, R., Chávez, E., Crochemore, M. (eds.) CPM 2003. LNCS, vol. 2676, pp. 170-185. Springer, Heidelberg (2003)
8. Moret, B.M.E.,Warnow, T.: Advances in phylogeny reconstruction from gene order and content data. In: Zimmer, E.A., Roalson, E.H. (eds.) Molecular Evolution: Producing the Biochemical Data, Part B,Methods in Enzymology, vol. 395, pp. 673-700. Elsevier, Amsterdam (2005)
9. Palmer, J.D.: Chloroplast and mitochondrial genome evolution in land plants. In: Herrmann, R. (ed.) Cell Organelles, pp. 99-133. Springer, Heidelberg (1992)
10. Palmer, J.D., Thompson, W.F.: Rearrangements in the chloroplast genomes of mung beanand pea. Proc. Nat'l Acad. Sci., USA 78, 5533-5537 (1981)
11. Sankoff, D.: Edit distance for genome comparison based on non-local operations. In: Apostolico, A., Galil, Z., Manber, U., Crochemore, M. (eds.) CPM 1992. LNCS, vol. 644, pp. 121-135. Springer, Heidelberg (1992)
12. Sankoff, D., Goldstein, M.: Probabilistic models for genome shuffling. Bull. Math. Biol. 51, 117-124 (1989)
13. Sleator, D.D., Tarjan, R.E.: Self-adjusting binary search trees. J. ACM32(3), 652-686 (1985)
14. Sturtevant, A.H.: A crossover reducer in Drosophila melanogaster due to inversion of a section of the third chromosome. Biol. Zent. Bl. 46, 697-702 (1926)
15. Sturtevant, A.H., Dobzhansky, T.: Inversions in the third chromosome of wild races of drosophila pseudoobscura and their use in the study of the history of the species. Proc. Nat'l Acad. Sci., USA 22, 448-450 (1936)
16. Tannier, E., Bergeron, A., Sagot, M.-F.: Advances on sorting by reversals. Disc. Appl. Math. 155(6-7), 881-888 (2007)
17. Tannier, E., Sagot, M.-F.: Sorting by reversals in subquadratic time. In: Sahinalp, S.C., Muthukrishnan, S.M., Dogrusoz, U. (eds.) CPM 2004. LNCS, vol. 3109, pp. 1-13. Springer, Heidelberg (2004)