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Ultra-Perfect Sorting Scenarios

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Comparative Genomics (RECOMB-CG 2010)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 6398))

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Abstract

Perfection has been used as a criteria to select rearrangement scenarios since 2004. However, there is a fundamental bias towards extant species in the original definition: ancestral species are not bound to perfection. Here we develop a new theory of perfection that takes an egalitarian view of species, and apply it to the complex evolution of mammal chromosome X.

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References

  1. Bérard, S., Bergeron, A., Chauve, C.: Conservation of combinatorial structures in evolution scenarios. In: Lagergren, J. (ed.) RECOMB-WS 2004. LNCS (LNBI), vol. 3388, pp. 1–14. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  2. Bérard, S., Bergeron, A., Chauve, C., Paul, C.: Perfect sorting by reversals is not always difficult. IEEE/ACM Trans. Comput. Biology Bioinform. 4(1), 4–16 (2007)

    Article  Google Scholar 

  3. Bérard, S., Chateau, A., Chauve, C., Paul, C., Tannier, E.: Perfect DCJ rearrangement. In: Nelson, C.E., Vialette, S. (eds.) RECOMB-CG 2008. LNCS (LNBI), vol. 5267, pp. 158–169. Springer, Heidelberg (2008)

    Chapter  Google Scholar 

  4. Bergeron, A., Chauve, C., de Montgolfier, F., Raffinot, M.: Computing Common Intervals of k Permutations, with Applications to Modular Decomposition of Graphs. In: Brodal, G.S., Leonardi, S. (eds.) ESA 2005. LNCS, vol. 3669, pp. 779–790. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  5. Bourque, G., Pevzner, P.A., Tesler, G.: Reconstructing the genomic architecture of ancestral mammals: Lessons from human, mouse, and rat genomes. Genome Research 14(4), 507–516 (2004)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Braga, M.D., Gautier, C., Sagot, M.-F.: An asymmetric approach to preserve common intervals while sorting by reversals. Algorithms for Molecular Biology 4(16) (2009)

    Google Scholar 

  7. Figeac, M., Varré, J.-S.: Sorting by reversals with common intervals. In: Jonassen, I., Kim, J. (eds.) WABI 2004. LNCS (LNBI), vol. 3240, pp. 26–37. Springer, Heidelberg (2004)

    Chapter  Google Scholar 

  8. Heber, S., Stoye, J.: Finding all common intervals of k permutations. In: Amir, A., Landau, G.M. (eds.) CPM 2001. LNCS, vol. 2089, pp. 207–218. Springer, Heidelberg (2001)

    Chapter  Google Scholar 

  9. Hsu, W.-L.: PC-trees vs. PQ-trees. In: Wang, J. (ed.) COCOON 2001. LNCS, vol. 2108, pp. 207–217. Springer, Heidelberg (2001)

    Chapter  Google Scholar 

  10. Hsu, W.-L., McConnell, R.M.: PC trees and circular-ones arrangements. Theor. Comput. Sci. 296(1), 99–116 (2003)

    Article  Google Scholar 

  11. Landau, G.M., Parida, L., Weimann, O.: Using PQ trees for comparative genomics. In: Apostolico, A., Crochemore, M., Park, K. (eds.) CPM 2005. LNCS, vol. 3537, pp. 128–143. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  12. Sagot, M.-F., Tannier, E.: Perfect sorting by reversals. In: Wang, L. (ed.) COCOON 2005. LNCS, vol. 3595, pp. 42–51. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  13. Tesler, G.: GRIMM: genome rearrangements web server. Bioinformatics 18(3), 492–493 (2002)

    Article  CAS  PubMed  Google Scholar 

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Ouangraoua, A., Bergeron, A., Swenson, K.M. (2010). Ultra-Perfect Sorting Scenarios. 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_5

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  • DOI: https://doi.org/10.1007/978-3-642-16181-0_5

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-16180-3

  • Online ISBN: 978-3-642-16181-0

  • eBook Packages: Computer ScienceComputer Science (R0)

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