Inversion medians outperform breakpoint medians in phylogeny reconstruction from gene-order data

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

Volumn 2452, Issue , 2002, Pages 521-536

  Moret, Bernard M E ^a   Siepel, Adam C ^b   Tang, Jijun ^a   Liu, Tao ^a  

^a MSC01 1070   (United States)

^b University of California Santa Cruz   (United States)

Author keywords

Breakpoint; Genome rearrangement; Genomic distance; Inversion; Reversal

Indexed keywords

BIOINFORMATICS; BIOLOGY; FORESTRY; GENES; SOFTWARE TESTING;

BREAKPOINT; GENOME REARRANGEMENTS; GENOMIC DISTANCE; INVERSION; REVERSAL;

EVOLUTIONARY ALGORITHMS;

EID: 84957042462     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/3-540-45784-4_40     Document Type: Conference Paper

References (27)

1. D. Bader, B. Moret, and M. Yan. A fast linear-time algorithm for inversion distance with an experimental comparison. J. Comput. Biol., 8(5):483–491, 2001.
2. M. Blanchette, G. Bourque, and D. Sankoff. Breakpoint phylogenies. In S. Miyano and T. Takagi, editors, Genome Informatics 1997, pages 25–34. Univ. Academy Press, 1997.
3. G. Bourque and P. Pevzner. Genome-scale evolution: reconstructing gene orders in the ancestral species. Genome Research, 12:26–36, 2002.
4. A. Caprara. Formulations and hardness of multiple sorting by reversals. In Proc. 3rd Int’l Conf. on Comput. Mol. Biol. RECOMB99, pages 84–93. ACM Press, 1999.
5. A. Caprara. On the practical solution of the reversal median problem. In Proc. 1st Workshop on Algs. in Bioinformatics WABI 2001, volume 2149 of Lecture Notes in Computer Science, pages 238–251. Springer-Verlag, 2001.
6. M. Cosner, R. Jansen, B. Moret, L. Raubeson, L. 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 Proc. 8th Int’l Conf. on Intelligent Systems for Mol. Biol. ISMB-2000, pages 104–115, 2000.
7. S. Downie and J. Palmer. Use of chloroplast DNA rearrangements in reconstructing plant phylogeny. In P. Soltis, D. Soltis, and J. Doyle, editors, Plant Molecular Systematics, pages 14–35. Chapman and Hall, 1992.
8. N. El-Mabrouk. Genome rearrangement by reversals and insertions/deletions of contiguous segments. In Proc. 11th Ann. Symp. Combin. Pattern Matching CPM 00, volume 1848 of Lecture Notes in Computer Science, pages 222–234. Springer- Verlag, 2000.
9. S. Hannenhalli and P. Pevzner. Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals). In Proc. 27th Ann. Symp. Theory of Computing STOC 95, pages 178–189. ACM Press, 1995.
10. S. Hannenhalli and P. Pevzner. Transforming mice into men (polynomial algorithm for genomic distance problems). In Proc. 36th Ann. IEEE Symp. Foundations of Comput. Sci. FOCS 95, pages 581–592. IEEE Press, 1995.
11. B. Larget, J. Kadane, and D. Simon. A Markov chain Monte Carlo approach to reconstructing ancestral genome rearrangements. Technical Report, Carnegie Mellon University, Pittsburgh, PA, 2002. Available at www.stat.cmu.edu/tr/tr765/.
12. B. Moret, J. Tang, L.-S. Wang, and T. Warnow. Steps toward accurate reconstructions of phylogenies from gene-order data. J. Comput. Syst. Sci., 2002. in press.
13. B. Moret, L.-S. Wang, T. Warnow, and S. Wyman. New approaches for reconstructing phylogenies from gene-order data. In Proc. 9th Int’l Conf. on Intelligent Systems for Mol. Biol. ISMB 2001, volume 17 of Bioinformatics, pages S165–S173, 2001.
14. B. Moret, S. Wyman, D. Bader, T. Warnow, and M. Yan. A new implementation and detailed study of breakpoint analysis. In Proc. 6th Pacific Symp. Biocomputing PSB 2001, pages 583–594. World Scientific Pub., 2001.
15. J. Nadeau and B. Taylor. Lengths of chromosome segments conserved since divergence of man and mouse. Proc. Nat’l Acad. Sci. USA, 81:814–818, 1984.
16. R. Olmstead and J. Palmer. Chloroplast DNA systematics: a review of methods and data analysis. Amer. J. Bot., 81:1205–1224, 1994.
17. J. Palmer. Chloroplast and mitochondrial genome evolution in land plants. In R. Herrmann, editor, Cell Organelles, pages 99–133. Springer Verlag, 1992.
18. I. Pe’er and R. Shamir. The median problems for breakpoints are NP-complete. Elec. Colloq. on Comput. Complexity, 71, 1998.
19. L. Raubeson and R. Jansen. Chloroplast DNA evidence on the ancient evolutionary split in vascular land plants. Science, 255:1697–1699, 1992.
20. L. A. Raubeson, B. M. Moret, J. Tang, S. K. Wyman, and T. Warnow. Inferring phylogenetic relationships using whole genome data: A case study of photosynthetic organelles and chloroplast genomes. Technical Report TR-CS-2001-19, U. of New Mexico, Albuquerque, New Mexico, 2001.
21. D. Sankoff and M. Blanchette. Multiple genome rearrangement and breakpoint phylogeny. J. Comp. Biol., 5:555–570, 1998.
22. A. Siepel. Exact algorithms for the reversal median problem. Master’s thesis, U. New Mexico, Albuquerque, NM, 2001. Available at www.cs.unm.edu/∼acs/thesis.html.
23. A. Siepel. An algorithm to find all sorting reversals. In Proc. 6th Int’l Conf. on Comput. Mol. Biol. RECOMB02. ACM Press, 2002. to appear.
24. A. Siepel and B. Moret. Finding an optimal inversion median: experimental results. In Proc. 1st Workshop on Algs. in Bioinformatics WABI 2001, volume 2149 of Lecture Notes in Computer Science, pages 189–203. Springer-Verlag, 2001.
25. D. Swofford, G. Olson, P. Waddell, and D. Hillis. Phylogenetic inference. In D. Hillis, C. Moritz, and B. Mable, editors, Molecular Systematics, 2nd ed., chapter 11. Sinauer Associates, 1996.
26. L.-S. Wang, R. Jansen, B. Moret, L. Raubeson, and T. Warnow. Fast phylogenetic methods for the analysis of genome rearrangement data: an empirical study. In Proc. 7th Pacific Symp. Biocomputing PSB 2002, pages 524–535. World Scientific Pub., 2002.
27. L.-S. Wang and T. Warnow. Estimating true evolutionary distances between genomes. In Proc. 33rd Symp. on Theory of Comp. STOC01, pages 637–646. ACM Press, 2001.