Genome halving and double distance with losses

Journal of Computational Biology

Volumn 18, Issue 9, 2011, Pages 1185-1199

  Savard, Olivier Tremblay ^a   Gagnon, Yves ^a   Bertrand, Denis ^a   El Mabrouk, Nadia ^a  

^a UNIVERSITÉ DE MONTRÉAL   (Canada)

Author keywords

DCJ; distance; genome duplication; genome halving; losses; rearrangement

Indexed keywords

ALGORITHM; BIOLOGICAL MODEL; CHROMOSOME; COMPUTER SIMULATION; CONFERENCE PAPER; GENE DOSAGE; GENE DUPLICATION; GENE REARRANGEMENT; GENETICS; GENOME; MOLECULAR EVOLUTION; MUTATION; PHYLOGENY; PLOIDY;

ALGORITHMS; CHROMOSOMES; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; GENE DOSAGE; GENE DUPLICATION; GENE REARRANGEMENT; GENOME; MODELS, GENETIC; MUTATION; PHYLOGENY; PLOIDIES;

EID: 80052630417     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2011.0136     Document Type: Conference Paper

References (24)

1. Alekseyev, M., and Pevzner, P. 2007a. Colored de Bruijn graphs and the genome halving problem. IEEE/ACM Trans. Comput. Biol. Bioinform. 4, 98-107. (Pubitemid 46375819)
2. Alekseyev, M., and Pevzner, P. 2007b. Whole genome duplications, multi-break rearrangements, and genome halving problem. Proc. 18th Annu. ACM-SIAM Symp. Discrete Algorithms 665-679.
3. Bader, D., Moret, B., and Yan, M. 2001. A linear-time algorithm for computing inversion distance between signed permutations with an experimental study. J. Comput. Biol. 8, 483-491. (Pubitemid 33044073)
4. Bergeron, A., Mixtacki, J., and Stoye, J. 2004. Reversal distance without hurdles and fortresses. Lect. Notes Comput. Sci. 3109, 388-399.
5. Bergeron, A., Mixtacki, J., and Stoye, J. 2006. A unifying view of genome rearrangements. Lect. Notes Comput. Sci. 4175, 163-173. (Pubitemid 44609667)
6. Bergeron, A., Mixtacki, J., and Stoye, J. 2009. A new linear time algorithm to compute the genomic distance via the double cut andjoin distance. Theoret. Comput. Sci. 410, 5300-5316.
7. Blanc, G., Hokamp, K., and Wolfe, K. 2003. A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Res. 13, 137-144. (Pubitemid 36575763)
8. Bowers, J., Chapman, B., Romg, J., et al. 2003. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422, 433-438. (Pubitemid 36411396)
9. Dehal, P., J.B. 2005. Two rounds of whole genome duplication in the ancestral vertebrate. Plos Biol. 3, e314.
10. El-Mabrouk, N., and Sankoff, D. 2003. The reconstruction of doubled genomes. SIAM J. Comput. 32, 754-792.
11. Gavranović, H., and Tannier, E. 2010. Guided genome halving: probably optimal solutions provide good insights into the preduplication ancestral genome of Saccharomyces cerevisiae. Pac. Symp. Biocomput. 15, 21-30.
12. Gordon, J., Byrne, K., and Wolfe, K. 2009. Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome. Plo S Genet. 5, e1000485.
13. Hannenhalli, S. 1995. Polynomial-time algorithm for computing translocation distance between genomes. Lect. Notes Comput. Sci. 937, 162-176.
14. Hannenhalli, S., and Pevzner, P. 1995. Transforming men into mice. Proc. IEEE 36th Annu. Symp. Found. Comput. Sci. 581-592.
15. Hannenhalli, S., and Pevzner, P.A. 1999. Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals). J. ACM 48, 1-27.
16. Kotzig, A. 1968. Moves without forbidden transitions in a graph. Matematicky Casopis 18, 76-80.
17. Pevzner, P. 1995. DNA physical mapping and alternating eulerian cycles in colored graphs. Algorithmica 13, 77-105.
18. Salse, J., Bolot, S., Throude, M., et al. 2008. Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution. Plant Cell 20, 11-24. (Pubitemid 352844030)
19. Soltis, D., Albert, V., Leebens-Mack, J., et al. 2009. Polyploidy and angiosperm diversification. Am. J. Botany 96, 336-348.
20. Tannier, E., Zheng, C., and Sankoff, D. 2009. Multichromosomal median and halving problems under different genomic distances. BMC Bioinform. 10.
21. Tesler, G 2002. Efficient algorithms for multichromosomal genome rearrangements. J. Comput. Syst. Sci. 65, 587-609.
22. Yancopoulos, S., Attie, O., and Friedberg, R. 2005. Efficient sorting of genomic permutations by translocation, inversion and block interchange. Bioinformatics 21, 3340-3346. (Pubitemid 41222437)
23. Zheng, C., Zhu, Q., Adam, Z., et al. 2008a. Guided genome halving: hardness, heuristics and the history of the hemiascomycetes. Proc. ISMB 96-104.
24. Zheng, C., Zhu, Q., and Sankoff, D. 2008b. Descendants of whole genome duplication within gene order phylogeny. J. Comput. Biol. 15, 947-964.