Abstract
The double-cut-and-join operation (DCJ) is a fundamental graph operation that is used to model a variety of genome rearrangements. However, DCJs are only useful when comparing genomes with equal (or nearly equal) gene content. One obvious extension of the DCJ framework supplements DCJs with insertions and deletions of chromosomes and chromosomal intervals, which implies a model in which DCJs receive unit cost, whereas insertions and deletions receive a nonnegative cost of ω. This paper proposes a unified model finding a minimum-cost transformation of one genome (with circular chromosomes) into another genome for any value of ω. In the process, it resolves the open case ω > 1.
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References
Arndt, W., Tang, J.: Emulating insertion and deletion events in genome rearrangement analysis. In: 2011 IEEE International Conference on Bioinformatics and Biomedicine, pp. 105–108 (2011)
Bafna, V., Pevzner, P.A.: Genome rearrangements and sorting by reversals. SIAM J. Comput. 25(2), 272–289 (1996)
Bergeron, A., Mixtacki, J., Stoye, J.: A unifying view of genome rearrangements. In: Bücher, P., Moret, B.M.E. (eds.) WABI 2006. LNCS (LNBI), vol. 4175, pp. 163–173. Springer, Heidelberg (2006)
Braga, M., Machado, R., Ribeiro, L., Stoye, J.: On the weight of indels in genomic distances. BMC Bioinformatics 12(suppl. 9), S13 (2011)
Braga, M.D.V., Willing, E., Stoye, J.: Genomic distance with DCJ and indels. In: Moulton, V., Singh, M. (eds.) WABI 2010. LNCS, vol. 6293, pp. 90–101. Springer, Heidelberg (2010)
Compeau, P.: DCJ-indel sorting revisited. Algorithms for Molecular Biology 8(1), 6 (2013)
Compeau, P.E.C.: A simplified view of DCJ-indel distance. In: Raphael, B., Tang, J. (eds.) WABI 2012. LNCS, vol. 7534, pp. 365–377. Springer, Heidelberg (2012)
Dobzhansky, T., Sturtevant, A.H.: Inversions in the chromosomes of drosophila pseudoobscura. Genetics 23(1), 28–64 (1938)
Fertin, G., Labarre, A., Rusu, I., Tannier, E., Vialette, S.: Combinatorics of Genome Rearrangements. MIT Press (2009)
da Silva, P.H., Braga, M.D.V., Machado, R., Dantas, S.: DCJ-indel distance with distinct operation costs. In: Raphael, B., Tang, J. (eds.) WABI 2012. LNCS, vol. 7534, pp. 378–390. Springer, Heidelberg (2012)
Yancopoulos, S., Attie, O., Friedberg, R.: Efficient sorting of genomic permutations by translocation, inversion and block interchange. Bioinformatics 21(16), 3340–3346 (2005)
Yancopoulos, S., Friedberg, R.: DCJ path formulation for genome transformations which include insertions, deletions, and duplications. Journal of Computational Biology 16(10), 1311–1338 (2009)
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Compeau, P.E.C. (2014). A Generalized Cost Model for DCJ-Indel Sorting. In: Brown, D., Morgenstern, B. (eds) Algorithms in Bioinformatics. WABI 2014. Lecture Notes in Computer Science(), vol 8701. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-44753-6_4
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DOI: https://doi.org/10.1007/978-3-662-44753-6_4
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