Abstract
Large-scale mutational events that occur when stretches of DNA sequence move throughout genomes are called genome rearrangement events. In bacteria, inversions are one of the most frequently observed rearrangements. In some bacterial families, inversions are biased in favor of symmetry as shown by recent research [6, 8, 10]. In addition, several results suggest that short segment inversions are more frequent in the evolution of microbial genomes [4,6,15]. Despite the fact that symmetry and length of the reversed segments seem very important, they have not been considered together in any problem in the genome rearrangement field. Here, we define the problem of sorting genomes (or permutations) using inversions whose costs are assigned based on their lengths and asymmetries. We present five procedures and we assess these procedure performances on small sized permutations. The ideas presented in this paper provide insights to solve the problem and set the stage for a proper theoretical analysis.
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References
Arruda, T.S., Dias, U., Dias, Z.: Heuristics for the sorting by length-weighted inversion problem. In: Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics, pp. 498–507 (2013)
Arruda, T.S., Dias, U., Dias, Z.: Heuristics for the sorting by length-weighted inversions problem on signed permutations. In: Dediu, A.-H., Martín-Vide, C., Truthe, B. (eds.) AlCoB 2014. LNCS, vol. 8542, pp. 59–70. Springer, Heidelberg (2014)
Bender, M.A., Ge, D., He, S., Hu, H., Pinter, R.Y., Skiena, S., Swidan, F.: Improved bounds on sorting by length-weighted reversals. Journal of Computer and System Sciences 74(5), 744–774 (2008)
Blanchette, M., Kunisawa, T., Sankoff, D.: Parametric genome rearrangement. Gene 172(1), C11–C17 (1996)
Caprara, A.: Sorting permutations by reversals and Eulerian cycle decompositions. SIAM Journal on Discrete Mathematics 12(1), 91–110 (1999)
Darling, A.E., Miklós, I., Ragan, M.A.: Dynamics of genome rearrangement in bacterial populations. PLoS Genetics 4(7), e1000128 (2008)
Dias, U., Baudet, C., Dias, Z.: Greedy randomized search procedure to sort genomes using symmetric, almost-symmetric and unitary inversions. In: Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics, BCB 2013, pp. 181–190. ACM, New York (2013)
Dias, U., Dias, Z., Setubal, J.C.: A simulation tool for the study of symmetric inversions in bacterial genomes. In: Tannier, E. (ed.) RECOMB-CG 2010. LNCS, vol. 6398, pp. 240–251. Springer, Heidelberg (2010)
Dias, Z., Dias, U., Setubal, J.C., Heath, L.S.: Sorting genomes using almost-symmetric inversions. In: Proceedings of the 27th Symposium On Applied Computing (SAC 2012), Riva del Garda, Italy, pp. 1–7 (2012)
Eisen, J.A., Heidelberg, J.F., White, O., Salzberg, S.L.: Evidence for symmetric chromosomal inversions around the replication origin in bacteria. Genome Biology 1(6), research0011.1–research0011.9 (2000)
Hannenhalli, S., Pevzner, P.A.: Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals. Journal of the ACM 46(1), 1–27 (1999)
Lefebvre, J.F., El-Mabrouk, N., Tillier, E., Sankoff, D.: Detection and validation of single gene inversions. Bioinformatics 19(suppl 1), i190–196 (2003)
Ohlebusch, E., Abouelhoda, M.I., Hockel, K., Stallkamp, J.: The median problem for the reversal distance in circular bacterial genomes. In: Apostolico, A., Crochemore, M., Park, K. (eds.) CPM 2005. LNCS, vol. 3537, pp. 116–127. Springer, Heidelberg (2005)
Pinter, R.Y., Skiena, S.: Genomic sorting with length-weighted reversals. Genome Informatics 13, 2002 (2002)
Sankoff, D.: Short inversions and conserved gene cluster. Bioinformatics 18(10), 1305–1308 (2002)
Sankoff, D., Lefebvre, J.F., Tillier, E., Maler, A., El-Mabrouk, N.: The distribution of inversion lengths in bacteria. In: Lagergren, J. (ed.) RECOMB-WS 2004. LNCS (LNBI), vol. 3388, pp. 97–108. Springer, Heidelberg (2005)
Swidan, F., Bender, M., Ge, D., He, S., Hu, H., Pinter, R.: Sorting by length-weighted reversals: Dealing with signs and circularity. In: Sahinalp, S.C., Muthukrishnan, S.M., Dogrusoz, U. (eds.) CPM 2004. LNCS, vol. 3109, pp. 32–46. Springer, Heidelberg (2004)
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Baudet, C., Dias, U., Dias, Z. (2014). Length and Symmetry on the Sorting by Weighted Inversions Problem. In: Campos, S. (eds) Advances in Bioinformatics and Computational Biology. BSB 2014. Lecture Notes in Computer Science(), vol 8826. Springer, Cham. https://doi.org/10.1007/978-3-319-12418-6_13
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DOI: https://doi.org/10.1007/978-3-319-12418-6_13
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