Abstract
Genome rearrangements have been modeled by a variety of operations such as inversions, translocations, fissions, fusions, transpositions and block interchanges. The double cut and join operation, introduced by Yancopoulos et al., allows to model all the classical operations while simplifying the algorithms. In this paper we show a simple way to apply this operation to the most general type of genomes with a mixed collection of linear and circular chromosomes. We also describe a graph structure that allows simplifying the theory and distance computation considerably, as neither capping nor concatenation of the linear chromosomes are necessary.
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References
Sankoff, D., Mazowita, M.: Stability of rearrangement measures in the comparison of genome sequences. In: Miyano, S., Mesirov, J., Kasif, S., Istrail, S., Pevzner, P.A., Waterman, M. (eds.) RECOMB 2005. LNCS (LNBI), vol. 3500, pp. 603–614. Springer, Heidelberg (2005)
Bergeron, A., Stoye, J.: On the similarity of sets of permutations and its applications to genome comparison. In: Warnow, T.J., Zhu, B. (eds.) COCOON 2003. LNCS, vol. 2697, pp. 68–79. Springer, Heidelberg (2003)
Yancopoulos, S., Attie, O., Friedberg, R.: Efficient sorting of genomic permutations by translocation, inversion and block interchange. Bioinformatics 21, 3340–3346 (2005)
Casjens, S., Palmer, N., van Vugt, R., Huang, W.M., Stevenson, B., Rosa, P., Lathigra, R., Sutton, G., Peterson, J., Dodson, R.J., Haft, D., Hickey, E., Gwinn, M., White, O., Fraser, C.M.: A bacterial genome in flux: The twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi. Mol. Microbiol. 35, 490–516 (2000)
Volff, J.N., Altenbuchner, J.: A new beginning with new ends: Linearisation of circular chromosomes during bacterial evolution. FEMS Microbiol. Lett. 186, 143–150 (2000)
Zheng, C., Lenert, A., Sankoff, D.: Reversal distance for partially ordered genomes. Bioinformatics 21, i502–i508 (2005) (proceedings of ISMB 2005)
El-Mabrouk, N.: Genome rearrangements with gene families. In: Gascuel, O. (ed.) Mathematics of Evolution and Phylogeny, pp. 291–320. Oxford University Press, Oxford (2005)
Hannenhalli, S., Pevzner, P.A.: Transforming men into mice (polynomial algorithm for genomic distance problem). In: Proceedings of FOCS 1995, pp. 581–592. IEEE Press, Los Alamitos (1995)
Lu, L., Huang, Y.L., Wang, T.C., Chiu, H.T.: Analysis of circular genome rearrangement by fusions, fissions and block-interchanges. BMC Bioinformatics 7 (2006)
Lin, Y.C., Lu, C.L., Chang, H.Y., Tang, C.Y.: An efficient algorithm for sorting by block-interchanges and its application to the evolution of vibrio species. J. Comp. Biol. 12, 102–112 (2005)
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Bergeron, A., Mixtacki, J., Stoye, J. (2006). A Unifying View of Genome Rearrangements. In: Bücher, P., Moret, B.M.E. (eds) Algorithms in Bioinformatics. WABI 2006. Lecture Notes in Computer Science(), vol 4175. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11851561_16
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DOI: https://doi.org/10.1007/11851561_16
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-39583-6
Online ISBN: 978-3-540-39584-3
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