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Transposition Diameter and Lonely Permutations

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Advances in Bioinformatics and Computational Biology (BSB 2012)

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Abstract

Determining the transposition distance of permutations was proven recently to be \(\textup{NP}\)-hard. However, the problem of the transposition diameter is still open. The known lower bounds for the diameter were given by Meidanis, Walter and Dias when the lengths of the permutations are even and by Elias and Hartman when the lengths are odd. A better lower bound for the transposition diameter was proposed using the new definition of super-bad permutations, that would be a particular family of the lonely permutations. We show that there are no super-bad permutations, by computing the exact transposition distance of the union of two copies of particular lonely permutations that we call knot permutations. Meidanis, Walter, Dias, Elias and Hartman, therefore, still hold the current best lower bound. Moreover, we consider the union of distinct lonely permutations and manage to define an alternative family of permutations that meets the current lower bound.

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References

  1. Bafna, V., Pevzner, P.A.: Sorting by Transpositions. SIAM J. Disc. Math. 11, 224–240 (1998)

    Article  MathSciNet  MATH  Google Scholar 

  2. Boore, J.L.: The duplication/random loss model for gene rearrangement exemplified by mitochondrial genomes of deuterostome animals. In: Comparative Genomics, pp. 133–148. Kluwer Academic Publishers (2000)

    Google Scholar 

  3. Bulteau, L., Fertin, G., Rusu, I.: Sorting by Transpositions Is Difficult. In: Aceto, L., Henzinger, M., Sgall, J. (eds.) ICALP 2011, Part I. LNCS, vol. 6755, pp. 654–665. Springer, Heidelberg (2011)

    Chapter  Google Scholar 

  4. Christie, D.A.: Genome Rerrangement Problems. Ph.D. dissertation, University of Glasgow, Scotland (1999)

    Google Scholar 

  5. Dias, Z.: Rearranjo de genomas: uma coletânea de artigos. Ph.D. dissertation, UNICAMP, Brazil (2002)

    Google Scholar 

  6. Elias, I., Hartman, T.: A 1.375-approximation algorithm for sorting by transpositions. IEEE/ACM Trans. Comput. Biol. Bioninformatics 3(4), 369–379 (2006)

    Article  Google Scholar 

  7. Eriksson, H., Eriksson, K., Karlander, J., Svensson, L., Wästlund, J.: Sorting a bridge hand. Discrete Math. 241(1), 289–300 (2001)

    Article  MathSciNet  MATH  Google Scholar 

  8. Fortuna, V.J.: Distâncias de Transposição entre Genomas. Master dissertation, Instituto de Computação – UNICAMP, Brazil (2005)

    Google Scholar 

  9. Hausen, R.A., Faria, L., de Figueiredo, C.M.H., Kowada, L.A.B.: On the Toric Graph as a Tool to Handle the Problem of Sorting by Transpositions. In: Bazzan, A.L.C., Craven, M., Martins, N.F. (eds.) BSB 2008. LNCS (LNBI), vol. 5167, pp. 79–91. Springer, Heidelberg (2008)

    Chapter  Google Scholar 

  10. Hausen, R.A., Faria, L., de Figueiredo, C.M.H., Kowada, L.A.B.: Unitary Toric Classes, the Reality and Desire Diagram, and Sorting by Transpositions. SIAM J. Disc. Math. 24(3), 792–807 (2010)

    Article  MATH  Google Scholar 

  11. Kowada, L.A.B., Hausen, R.A., de Figueiredo, C.M.H.: Bounds on the Transposition Distance for Lonely Permutations. In: Ferreira, C.E., Miyano, S., Stadler, P.F. (eds.) BSB 2010. LNCS, vol. 6268, pp. 35–46. Springer, Heidelberg (2010)

    Chapter  Google Scholar 

  12. Lu, L., Yang, Y.: A Lower Bound on the Transposition Diameter. SIAM J. Disc. Math. 24(4), 1242–1249 (2010)

    Article  MathSciNet  MATH  Google Scholar 

  13. Meidanis, J., Walter, M.E.M.T., Dias, Z.: Transposition distance between a permutation and its reverse. In: Proceedings of the 4th South American Workshop on String Processing, pp. 70–79. Carleton University Press, Valparaíso (1997)

    Google Scholar 

  14. Sankoff, D., Leduc, G., Antoine, N., Paquin, B., Lang, B.F., Cedergren, R.: Gene sort comparisons for phylogenetic inference: evolution of the mitochondrial genome. Proc. Natl. Acad. Sci. 89(14), 6575–6579 (1992)

    Article  Google Scholar 

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Cunha, L.F.I., Kowada, L.A.B., de A. Hausen, R., de Figueiredo, C.M.H. (2012). Transposition Diameter and Lonely Permutations. In: de Souto, M.C., Kann, M.G. (eds) Advances in Bioinformatics and Computational Biology. BSB 2012. Lecture Notes in Computer Science(), vol 7409. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-31927-3_1

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  • DOI: https://doi.org/10.1007/978-3-642-31927-3_1

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-31926-6

  • Online ISBN: 978-3-642-31927-3

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