Abstract
A previous work of Braga, Willing and Stoye compared two genomes with unequal content, but without duplications, and presented a new linear time algorithm to compute the genomic distance, considering double cut and join (DCJ) operations, insertions and deletions. Here we derive from this approach an algorithm to sort one genome into another one also using DCJ, insertions and deletions. The optimal sorting scenarios can have different compositions and we compare two types of sorting scenarios: one that maximizes and one that minimizes the number of DCJ operations with respect to the number of insertions and deletions.
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References
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)
Blanc, G., et al.: Reductive genome evolution from the mother of Rickettsia. PLoS Genetics 3(1), e14 (2007)
Braga, M.D.V., Stoye, J.: The solution space of sorting by DCJ. To appear in Journal of Computational Biology (2010)
Braga, M.D.V., Willing, E., Stoye, J.: Genomic distance with DCJ and indels. In: Proceedings of WABI (to appear, 2010)
El-Mabrouk, N.: Sorting Signed Permutations by Reversals and Insertions/Deletions of Contiguous Segments. Journal of Discrete Algorithms 1(1), 105–122 (2001)
Hannenhalli, S., Pevzner, P.: Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals). Journal of the ACM 46, 1–27 (1999)
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)
Tannier, E., Zheng, C., Sankoff, D.: Multichromosomal median and halving problems under different genomic distances. BMC Bioinformatics 10, 120 (2009); Preliminary version in Crandall, K.A., Lagergren, J. (eds.): WABI 2008. LNCS (LNBI), vol. 5251, pp. 1–13. Springer, Heidelberg (2008)
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); Preliminary version in Nelson, C.E., Vialette, S. (eds.): RECOMB-CG 2008. LNCS (LNBI), vol. 5267, pp. 170–183. Springer, Heidelberg (2008)
Yancopoulos, S., Attie, O., Friedberg, R.: Efficient sorting of genomic permutations by translocation, inversion and block interchange. Bioinformatics 21, 3340–3346 (2005)
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Braga, M.D.V. (2010). On Sorting Genomes with DCJ and Indels. In: Tannier, E. (eds) Comparative Genomics. RECOMB-CG 2010. Lecture Notes in Computer Science(), vol 6398. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-16181-0_6
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DOI: https://doi.org/10.1007/978-3-642-16181-0_6
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-16180-3
Online ISBN: 978-3-642-16181-0
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