Abstract
In comparative genomics studies, finding a minimum length sequences of reversals, so called sorting by reversals, has been the topic of a huge literature. Since there are many minimum length sequences, another important topic has been the problem of listing all parsimonious sequences between two genomes, called the All Sorting Sequences by Reversals (ASSR) problem. In this paper, we revisit the ASSR problem for uni-chromosomal genomes when no duplications are allowed and when the relative order of the genes is known. We put the current body of work in perspective by illustrating the fundamental framework that is common for all of them, a perspective that allows us for the first time to theoretically compare their running times. The paper also proposes an improved framework that empirically speeds up all known algorithms.
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Ajana, Y., Lefebvre, J.-F., Tillier, E.R.M., El-Mabrouk, N.: Exploring the set of all minimal sequences of reversals - an application to test the replication-directed reversal hypothesis. In: GuigĂ³, R., Gusfield, D. (eds.) WABI 2002. LNCS, vol. 2452, pp. 300–315. Springer, Heidelberg (2002)
Baudet, C., Dias, Z.: An improved algorithm to enumerate all traces that sort a signed permutation by reversals. In: Proc. the 2010 ACM Symposium on Applied Computing, pp. 1521–1525 (2010)
Bergeron, A., Chauve, C., Hartman, T., Saint-Onge, K.: On the properties of sequences of reversals that sort a signed permutation. In: JOBIM, pp. 99–108 (June 2002)
Braga, M.D.V.: Baobabluna: the solution space of sorting by reversals. Bioinformatics 25(14) (2009)
Braga, M.D.V., Gautier, C., Sagot, M.: An asymmetric approach to preserve common intervals while sorting by reversals. Algorithms for Molecular Biology 4(16) (2009)
Braga, M.D.V., Sagot, M., Scornavacca, C., Tannier, E.: The solution space of sorting by reversals. In: Măndoiu, I.I., Zelikovsky, A. (eds.) ISBRA 2007. LNCS (LNBI), vol. 4463, pp. 293–304. Springer, Heidelberg (2007)
Caprara, A.: Sorting by reversals is difficult. In: Proc. 1st Ann. Int’l Conf. Comput. Mol. Biol. (RECOMB 1997), pp. 75–83. ACM Press, New York (1997)
Cartier, P., Foata, D.: Problèmes combinatoires de commutation et réarrangements. Lecture Notes in Maths, vol. 85 (1969)
Diekert, V., Rozenberg, G.: The Book of Traces. World Scientific, Singapore (1995)
Brightwell, G., Winkler, P.: Counting linear extensions is #P-complete. In: Proc. of the twenty-third annual ACM symposium on Theory of Computing, New Orleans, Louisiana, United States, pp. 175–181 (1991)
Hannenhalli, S., Pevzner, P.A.: Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals). In: Proc. 27th Ann. ACM Symp. Theory of Comput. (STOC 1995), pp. 178–189. ACM Press, New York (1995)
Siepel, A.C.: An algorithm to find all sorting reversals. In: Proc. 6th Ann. Int’l Conf. Comput. Mol. Biol. (RECOMB 2002), pp. 281–290. ACM Press, New York (2002)
Swenson, K.M., Rajan, V., Lin, Y., Moret, B.M.E.: Sorting signed permutations by inversions in O(n logn) time. In: Batzoglou, S. (ed.) RECOMB 2009. LNCS, vol. 5541, pp. 386–399. Springer, Heidelberg (2009)
Swenson, K.M., Badr, G., Sankoff, D.: Listing all sorting reversals in quadratic time. In: Singh, M. (ed.) WABI 2010. LNCS, vol. 6293, pp. 102–110. Springer, Heidelberg (2010)
Swenson, K.M., Lin, Y., Rajan, V., Moret, B.M.E.: Hurdles hardly have to be heeded. In: Nelson, C.E., Vialette, S. (eds.) RECOMB-CG 2008. LNCS (LNBI), vol. 5267, pp. 239–249. Springer, Heidelberg (2008)
Tannier, E., Bergeron, A., Sagot, M.-F.: Advances on sorting by reversals. Disc. Appl. Math. 155(6-7), 881–888 (2007)
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Badr, G., Swenson, K.M., Sankoff, D. (2010). Listing All Parsimonious Reversal Sequences: New Algorithms and Perspectives. 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_4
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DOI: https://doi.org/10.1007/978-3-642-16181-0_4
Publisher Name: Springer, Berlin, Heidelberg
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