On the similarity of sets of permutations and its applications to genome comparison

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

Volumn 2697, Issue , 2003, Pages 68-79

  Bergeron, Anne ^a   Stoye, Jens ^b  

^a UNIVERSITÉ DU QUÉBEC À MONTRÉAL   (Canada)

^b BIELEFELD UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CLUSTERING ALGORITHMS;

BREAKPOINT DISTANCE; CONSERVED INTERVALS; GENOME COMPARISON; GENOME REARRANGEMENTS; GRAPHIC REPRESENTATION; ITS APPLICATIONS; LINEAR-TIME ALGORITHMS; MEASURES OF DISTANCE;

GENES;

EID: 35248882900     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/3-540-45071-8_9     Document Type: Article

References (22)

1. Y. Ajana, J.-F. Lefebvre, E. R. M. Tillier, and N. El-Mabrouk. Exploring the set of all minimal sequences of reversals - an application to test the replication-directed reversal hypothesis. In Proc. WABI 2002, volume 2452 of LNCS, pages 300-315. Springer Verlag, 2002.
2. 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):483-492, 2001.
3. V. Bafna and P. A. Pevzner. Sorting by transpositions. SIAM J. Disc. Math., 11(2):224-240, 1998.
4. A. Bergeron, S. Heber, and J. Stoye. Common intervals and sorting by reversals: A marriage of necessity. Bioinformatics, 18(Suppl. 2):S54-S63, 2002. (Proc. ECCB 2002).
5. A. Bergeron and J. Stoye. On the similarity of sets of permutations and its application to genome comparison. Report 2003-01, Technische Fakultät der Universität Bielefeld, 2003. (Available at www.techfak.uni-bielefeld.de/ stoye/rpublications/report2003-01.pdf).
6. M. Blanchette, T. Kunisawa, and D. Sankoff. Gene order breakpoint evidence in animal mitochondrial phylogeny. J. Mol. Evol., 49(2):193-203, 1999.
7. J. L. Boore. Mitochondrial gene arrangement source guide. www.jgi.doe.gov/programs/comparative/Mito_top_level.html.
8. K. S. Booth and G. S. Lueker. Testing for the consecutive ones property, interval graphs and graph planarity using PQ-tree algorithms. J. Comput. Syst. Sci., 13(3):335-379, 1976.
9. G. Bourque and P. A. Pevzner. Genome-scale evolution: Reconstructing gene orders in the ancestral species. Genome Res., 12(1):26-36, 2002.
10. D. A. Christie. Genome Rearrangement Problems. PhD thesis, The University of Glasgow, 1998.
11. S. Hannenhalli and P. A. Pevzner. Transforming men into mice (polynomial algorithm for genomic distance problem). In Proc. FOCS 1995, pages 581-592. IEEE Press, 1995.
12. S. Hannenhalli and P. A. Pevzner. Transforming cabbage into turnip: Polynomial algorithm for sorting signed permutations by reversals. J. ACM, 46(1):1-27, 1999.
13. S. Heber and J. Stoye. Finding all common intervals of k permutations. In Proc. CPM 2001, volume 2089 of LNCS, pages 207-218. Springer Verlag, 2001.
14. H. Kaplan, R. Shamir, and R. E. Tarjan. A faster and simpler algorithm for sorting signed permutations by reversals. SIAM J. Computing, 29(3):880-892, 1999.
15. J. D. Kececioglu and D. Sankoff. Efficient bounds for oriented chromosome inversion distance. In Proc. CPM 1994, volume 807 of LNCS, pages 307-325. Springer Verlag, 1994.
16. B. Larget, J. Kadane, and D. Simon. A Markov chain Monte Carlo approach to reconstructing ancestral genome rearrangements. Technical report, Carnegie Mellon University, Pittsburgh, 2002.
17. 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. WABI 2002, volume 2452 of LNCS, pages 521-536. Springer Verlag, 2002.
18. M. Ozery-Flato and R. Shamir. Two notes on genome rearrangements. J. Bioinf. Comput. Biol., to appear.
19. D. Sankoff. Short inversions and conserved gene clusters. Bioinformatics, 18(10):1305-1308, 2002.
20. A. Siepel. An algorithm to find all sorting reversals. In Proc. RECOMB 2002, pages 281-290. ACM Press, 2002.
21. G. Tesler. Efficient algorithms for multichromosomal genome rearrangement. J. Comput. Syst. Sci., 65(3):587-609, 2002.
22. T. Uno and M. Yagiura. Fast algorithms to enumerate all common intervals of two permutations. Algorithmica, 26(2):290-309, 2000.