Sorting signed permutations by inversions in O(nlogn) time

Journal of Computational Biology

Volumn 17, Issue 3, 2010, Pages 489-501

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

^a EPFL   (Switzerland)

Author keywords

Algorithms; Combinatorics; Computational molecular biology; Genomic rearrangements; Phylogenetic trees

Indexed keywords

ALGORITHM; BIOLOGY; CHROMOSOME INVERSION; CONFERENCE PAPER; GENETICS; METHODOLOGY; NUCLEOTIDE SEQUENCE; TIME;

ALGORITHMS; BASE SEQUENCE; CHROMOSOME INVERSION; COMPUTATIONAL BIOLOGY; TIME FACTORS;

EID: 77950836402     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2009.0184     Document Type: Conference Paper

References (19)

1. Bader, D., Moret, B., and Yan, M. 2001. A fast linear-time algorithm for inversion distance with an experimental comparison. J. Comput. Biol. 8, 483-491.
2. Bergeron, A., and Stoye, J. 2003. On the similarity of sets of permutations and its applications to genome comparison. Lect. Notes Comput. Sci. 2697, 68-79. (Pubitemid 36892219)
3. Bergeron, A., Heber, S., and Stoye, J. 2002. Common intervals and sorting by reversals: a marriage of necessity. Proc. 2nd Eur. Conf. Comput. Biol. 54-63. (Pubitemid 41073217)
4. Caprara, A. 1997. Sorting by reversals is difficult. Proc. RECOMB'97 75-83.
5. Day, W., and Sankoff, D. 1987. The computational complexity of inferring phylogenies from chromosome inversion data. J. Theor. Biol. 127, 213-218. (Pubitemid 17004339)
6. Fertin, G., Labarre, A., Rusu, I., et al. 2009. Combinatorics of Genome Rearrangements. MIT Press, Cambridge, MA.
7. Hannenhalli, S., and Pevzner, P. 1995. Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals). Proc. 27th Annu. ACM Symp. Theory Comput. 178-189. (Pubitemid 129592185)
8. Kaplan, H., and Verbin, E. 2003. Efficient data structures and a new randomized approach for sorting signed permutations by reversals. Lecture Notes Comput. Sci. 2676, 170-185. (Pubitemid 36769861)
9. Moret, B., and Shapiro, H. 1994. An empirical assessment of algorithms for constructing a minimum spanning tree. DIMACS Monog. 15, 99-117.
10. Moret, B., and Warnow, T. 2005. Advances in phylogeny reconstruction from gene order and content data. Methods Enzymol. 395, 673-700. (Pubitemid 40754392)
11. Palmer, J. 1992. Chloroplast and mitochondrial genome evolution in land plants, 99-133. In Herrmann, R., ed., Cell Organelles. Springer Verlag, New York.
12. Palmer, J., and Thompson, W. 1981. Rearrangements in the chloroplast genomes of mung bean and pea. Proc. Natl. Acad. Sci. USA 78, 5533-5537. (Pubitemid 12245185)
13. Sankoff, D. 1992. Edit distance for genome comparison based on non-local operations. Lect. Notes Comput. Sci. 644, 121-135.
14. Sankoff, D., and Goldstein, M. 1989. Probabilistic models for genome shuffling. Bull. Math. Biol. 51, 117-124.
15. Sleator, D., and Tarjan, R. 1985. Self-adjusting binary search trees. J. ACM 32, 652-686.
16. Sturtevant, A. 1926. A crossover reducer in Drosophila melanogaster due to inversion of a section of the third chromosome. Biol. Zent. Bl. 46, 697-702.
17. Sturtevant, A., and Dobzhansky, T. 1936. Inversions in the third chromosome of wild races of Drosophila pseudoobscura and their use in the study of the history of the species. Proc. Natl. Acad. Sci. USA 22, 448-450.
18. Tannier, E., and Sagot, M.-F. 2004. Sorting by reversals in subquadratic time. Lect. Notes Comput. Sci. 3109, 1-13. (Pubitemid 38945531)
19. Tannier, E., Bergeron, A., and Sagot, M.-F. 2007. Advances on sorting by reversals. Disc. Appl. Math. 155, 881-888. (Pubitemid 46215773)