Abstract
Motivated by the trend of genome sequencing without completing the sequence of the whole genomes, Muñoz et al. recently studied the problem of filling an incomplete multichromosomal genome (or scaffold) I with respect to a complete target genome G such that the resulting genomic distance between I′ and G is minimized, where I′ is the corresponding filled scaffold. We call this problem the one-sided scaffold filling problem. In this paper, we follow Muñoz et al. to investigate the scaffold filling problem under the breakpoint distance for the simplest unichromosomal genomes. When the input genome contains no gene repetition (i.e., is a fragment of a permutation), we show that the two-sided scaffold filling problem is polynomially solvable. However, when the input genome contains some genes which appear twice, even the one-sided scaffold filling problem becomes NP-complete. Finally, using the ideas for solving the two-sided scaffold filling problem under the breakpoint distance we show that the two-sided scaffold filling problem under the genomic/rearrangement distance is also polynomially solvable.
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References
Chain, P., Grafham, D., Fulton, R., FitzGerald, M., Hostetler, J., Muzny, D., Ali, J., et al.: Genome project standards in a new era of sequencing. Science 326, 236–237 (2009)
Chen, X., Zheng, J., Fu, Z., Nan, P., Zhong, Y., Lonardi, S., Jiang, T.: Computing the assignment of orthologous genes via genome rearrangement. In: Proc. of the 3rd Asia-Pacific Bioinformatics Conf. (APBC 2005), pp. 363–378 (2005)
Chrobak, M., Kolman, P., Sgall, J.: The greedy algorithm for the minimum common string partition problem. In: Jansen, K., Khanna, S., Rolim, J.D.P., Ron, D. (eds.) RANDOM 2004 and APPROX 2004. LNCS, vol. 3122, pp. 84–95. Springer, Heidelberg (2004)
Damaschke, P.: Minimum Common String Partition Parameterized. In: Crandall, K.A., Lagergren, J. (eds.) WABI 2008. LNCS (LNBI), vol. 5251, pp. 87–98. Springer, Heidelberg (2008)
Downey, R., Fellows, M.: Parameterized Complexity. Springer, Heidelberg (1999)
Garey, M.R., Johnson, D.S.: Computers and Intractability: A Guide to the Theory of NP-Completeness. W.H. Freeman, New York (1979)
Goldstein, A., Kolman, P., Zheng, J.: Minimum common string partitioning problem: Hardness and approximations. In: Fleischer, R., Trippen, G. (eds.) ISAAC 2004. LNCS, vol. 3341, pp. 473–484. Springer, Heidelberg (2004); also in: The Electronic Journal of Combinatorics 12, paper R50 (2005)
Jiang, H., Zhu, B., Zhu, D., Zhu, H.: Minimum common string partition revisited. In: Lee, D.-T., Chen, D.Z., Ying, S. (eds.) FAW 2010. LNCS, vol. 6213, pp. 45–52. Springer, Heidelberg (2010)
Kaplan, H., Shafrir, N.: The greedy algorithm for edit distance with moves. Inf. Process. Lett. 97(1), 23–27 (2006)
Muñoz, A., Zheng, C., Zhu, Q., Albert, V., Rounsley, S., Sankoff, D.: Scaffold filling, contig fusion and gene order comparison. BMC Bioinformatics 11, 304 (2010)
Tesler, G.: Efficient algorithms for multichromosomal genome rearrangements. J. Computer and System Sciences 65, 587–609 (2002)
Watterson, G., Ewens, W., Hall, T., Morgan, A.: The chromosome inversion problem. J. Theoretical Biology 99, 1–7 (1982)
Yancopoulos, S., Attie, O., Friedberg, R.: Efficient sorting of genomic permutations by translocation, inversion and block interchange. Bioinformatics 21, 3340–3346 (2005)
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Jiang, H., Zheng, C., Sankoff, D., Zhu, B. (2010). Scaffold Filling under the Breakpoint Distance. 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_8
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DOI: https://doi.org/10.1007/978-3-642-16181-0_8
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