On sorting genomes with DCJ and indels

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

Volumn 6398 LNBI, Issue , 2010, Pages 62-73

  Braga, Marília D V ^a  

^a BIELEFELD UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DISTANCE; INSERTIONS AND DELETIONS; LINEAR-TIME ALGORITHMS; OPTIMAL SORTING; DOUBLE CUT AND JOINS;

ALGORITHMS; CONVOLUTIONAL CODES; CLUSTERING ALGORITHMS;

GENES;

EID: 78649911515     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-16181-0_6     Document Type: Conference Paper

References (12)

1. Bergeron, A., Mixtacki, J., Stoye, J.: A unifying view of genome rearrangements. In: Bücher, P., Moret, B.M.E. (eds.) WABI 2006. LNCS (LNBI), vol. 4175, pp. 163-173. Springer, Heidelberg (2006)
2. Blanc, G., et al.: Reductive genome evolution from the mother of Rickettsia. PLoS Genetics 3(1), e14 (2007)
3. Braga, M.D.V., Stoye, J.: The solution space of sorting by DCJ. To appear in Journal of Computational Biology (2010)
4. Braga, M.D.V., Willing, E., Stoye, J.: Genomic distance with DCJ and indels. In: Proceedings of WABI (to appear, 2010)
5. El-Mabrouk, N.: Sorting Signed Permutations by Reversals and Insertions/ Deletions of Contiguous Segments. Journal of Discrete Algorithms 1(1), 105-122 (2001)
6. Hannenhalli, S., Pevzner, P.: Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals). Journal of the ACM 46, 1-27 (1999)
7. Ouangraoua, A., Bergeron, A.: Parking functions, labeled trees and DCJ sorting scenarios. In: Ciccarelli, F.D., Miklós, I. (eds.) RECOMB-CG 2009. LNCS (LNBI), vol. 5817, pp. 24-35. Springer, Heidelberg (2009)
8. Tannier, E., Zheng, C., Sankoff, D.: Multichromosomal median and halving problems under different genomic distances. BMC Bioinformatics 10, 120 (2009);
9. Preliminary version in Crandall, K.A., Lagergren, J. (eds.):WABI 2008. LNCS (LNBI), vol. 5251, pp. 1-13. Springer, Heidelberg (2008)
10. Yancopoulos, S., Friedberg, R.: DCJ path formulation for genome transformations which include insertions, deletions, and duplications. Journal of Computational Biology 16(10), 1311-1338 (2009);
11. Preliminary version in Nelson, C.E., Vialette, S. (eds.): RECOMB-CG 2008. LNCS (LNBI), vol. 5267, pp. 170-183. Springer, Heidelberg (2008)
12. Yancopoulos, S., Attie, O., Friedberg, R.: Efficient sorting of genomic permutations by translocation, inversion and block interchange. Bioinformatics 21, 3340-3346 (2005) (Pubitemid 41222437)