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Notes on the \(\frac{6}{5}\)-Approximation Algorithm for One-Sided Scaffold Filling

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Frontiers in Algorithmics (FAW 2016)

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Abstract

We focus on designing algorithm for One-sided Scaffold Filling. Jiang et al. proposed a non-oblivious local search algorithm for this problem recently. We can give an example to show that this algorithm cannot approximate One-sided Scaffold Filling to \(\frac{6}{5}\). In this paper, we propose a new objective function based local search algorithm for One-sided Scaffold Filling, and give the accurate proof to show that its approximation ratio is \(\frac{6}{5}\).

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References

  1. Angibaud, S., Fertin, G., Rusu, I., Thevenin, A., Vialette, S.: On the approximability of comparing genomes with duplicates. J. Graph Algorithms Appl. 13(1), 19–53 (2009)

    Article  MathSciNet  MATH  Google Scholar 

  2. Blin, G., Fertin, G., Sikora, F., Vialette, S.: The Exemplar Breakpoint Distance for non-trivial genomes cannot be approximated. In: Das, S., Uehara, R. (eds.) WALCOM 2009. LNCS, vol. 5431, pp. 357–368. Springer, Heidelberg (2009)

    Chapter  Google Scholar 

  3. Cormode, G., Muthukrishnan, S.: The string edit distance matching problem with moves. In: Proceedings of 13th ACM-SIAM Symposium on Discrete Algorithms (SODA 2002), pp. 667–676 (2002)

    Google Scholar 

  4. Chen, Z., Fowler, R., Fu, B., Zhu, B.: On the inapproximability of the exemplar conserved interval distance problem of genomes. J. Comb. Optim. 15(2), 201–221 (2008)

    Article  MathSciNet  MATH  Google Scholar 

  5. Chen, Z., Fu, B., Zhu, B.: The approximability of the exemplar breakpoint distance problem. In: Cheng, S.-W., Poon, C.K. (eds.) AAIM 2006. LNCS, vol. 4041, pp. 291–302. Springer, Heidelberg (2006)

    Chapter  Google Scholar 

  6. Goldstein, A., Kolman, P., Zheng, J.: Minimum common string partition problem: hardness and approximations. In: Fleischer, R., Trippen, G. (eds.) ISAAC 2004. LNCS, vol. 3341, pp. 484–495. Springer, Heidelberg (2004)

    Chapter  Google Scholar 

  7. Jiang, M.: The zero exemplar distance problem. In: Tannier, E. (ed.) RECOMB-CG 2010. LNCS, vol. 6398, pp. 74–82. Springer, Heidelberg (2010)

    Chapter  Google Scholar 

  8. Jiang, H., Zheng, C., Sankoff, D., Zhu, B.: Scaffold filling under the breakpoint distance. In: Tannier, E. (ed.) RECOMB-CG 2010. LNCS, vol. 6398, pp. 83–92. Springer, Heidelberg (2010)

    Chapter  Google Scholar 

  9. Huson, D.H., Reinert, K., Myers, E.W.: The greedy path-merging algorithm for Contig scaffolding. J. ACM 49(5), 603–615 (2002)

    Article  MathSciNet  MATH  Google Scholar 

  10. Jiang, H., Zhong, F., Zhu, B.: Filling scaffolds with gene repetitions: maximizing the number of adjacencies. In: Giancarlo, R., Manzini, G. (eds.) CPM 2011. LNCS, vol. 6661, pp. 55–64. Springer, Heidelberg (2011)

    Chapter  Google Scholar 

  11. Jiang, H., Zheng, C., Sankoff, D., Zhu, B.: Scaffold filling under the breakpoint and related distances. IEEE/ACM Trans. Comput. Biol. Bioinform. 9(4), 1220–1229 (2012)

    Article  Google Scholar 

  12. Muñoz, A., Zheng, C., Zhu, Q., Albert, V., Rounsley, S., Sankoff, D.: Scaffold filling, contig fusion and gene order comparison. BMC Bioinform. 11, 304 (2010)

    Article  Google Scholar 

  13. Sankoff, D.: Genome rearrangement with gene families. Bioinformatics 15(11), 909–917 (1999)

    Article  Google Scholar 

  14. Liu, N., Jiang, H., Zhu, D., Zhu, B.: An improved approximation algorithm for scaffold filling to maximize the common adjacencies. IEEE/ACM TCBB 10(4), 905–913 (2013)

    MATH  Google Scholar 

  15. Liu, N., Zhu, D.: The algorithm for the two-sided scaffold filling problem. In: Chan, T.-H.H., Lau, L.C., Trevisan, L. (eds.) TAMC 2013. LNCS, vol. 7876, pp. 236–247. Springer, Heidelberg (2013)

    Chapter  Google Scholar 

  16. Jiang, H., Ma, J., Luan, J., Zhu, D.: Approximation and nonapproximability for the one-sided scaffold filling problem. In: Xu, D., Du, D., Du, D. (eds.) COCOON 2015. LNCS, vol. 9198, pp. 251–263. Springer, Heidelberg (2015)

    Chapter  Google Scholar 

  17. Caprara, A.: Sorting by reversals is difficult. In: Proceedings of RECOMB 1997, pp. 75–83 (1997)

    Google Scholar 

  18. Zhu, D., Wang, L.: On the complexity of unsigned translocation distance. Theor. Comput. Sci 352(1–3), 322–328 (2006)

    Article  MathSciNet  MATH  Google Scholar 

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Acknowledgments

This research is partially supported NSF of China under grant 61472222,61202014.

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Authors and Affiliations

  1. School of Computer Science and Technology, Shandong University, Jinan, 250101, People’s Republic of China

    Jingjing Ma & Haitao Jiang

Authors
  1. Jingjing Ma
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  2. Haitao Jiang
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Corresponding author

Correspondence to Haitao Jiang .

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Editors and Affiliations

  1. Shandong University, Jinan, China

    Daming Zhu

  2. MS EC-31, University of Texas at Dallas, Richardson, Texas, USA

    Sergey Bereg

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Ma, J., Jiang, H. (2016). Notes on the \(\frac{6}{5}\)-Approximation Algorithm for One-Sided Scaffold Filling. In: Zhu, D., Bereg, S. (eds) Frontiers in Algorithmics. FAW 2016. Lecture Notes in Computer Science(), vol 9711. Springer, Cham. https://doi.org/10.1007/978-3-319-39817-4_15

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  • DOI: https://doi.org/10.1007/978-3-319-39817-4_15

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-39816-7

  • Online ISBN: 978-3-319-39817-4

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