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Heuristics for the Sorting Signed Permutations by Reversals and Transpositions Problem

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Algorithms for Computational Biology (AlCoB 2018)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 10849))

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Abstract

We present two heuristics, Sliding Window and Look Ahead, to improve solutions for the Sorting Signed Permutations by Reversals and Transpositions Problem. To assess the heuristics, we implemented algorithms described in the literature to provide initial solutions. Despite the fact that we addressed a specific problem, both heuristics can be applied to many others within the area of genome rearrangement. When time is a crucial factor, Sliding Window is a better choice because it runs in linear time and improves the initial solutions in 76.4% of cases. If the quality of the solution is a priority, Look Ahead should be preferred because it improves the initial solutions in 97.6% of cases, but it runs in \(\mathcal {O}(n^3 \times alg(n))\), where alg(n) is the complexity of the algorithm given as input. By using these heuristics one may find a good tradeoff between running time and solution improvement.

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Acknowledgments

The authors acknowledge the support from CAPES, the International Cooperation Program CAPES/COFECUB Foundation under grant 831/15, the CNPq under grants 425340/2016-3, 400487/2016-0, 140466/2018-5, and 138219/2016-8 and also the São Paulo Research Foundation (FAPESP) under grants 2013/08293-7, 2014/19401-8, and 2015/11937-9.

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Authors and Affiliations

  1. Institute of Computing, University of Campinas, Albert Einstein 1251, Campinas, Brazil

    Klairton Lima Brito, Andre Rodrigues Oliveira & Zanoni Dias

  2. School of Technology, University of Campinas, Paschoal Marmo 1888, Limeira, Brazil

    Ulisses Dias

Authors
  1. Klairton Lima Brito
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  2. Andre Rodrigues Oliveira
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  3. Ulisses Dias
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  4. Zanoni Dias
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Corresponding author

Correspondence to Klairton Lima Brito .

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Editors and Affiliations

  1. The Hong Kong Polytechnic University, Kowloon, Hong Kong

    Jesper Jansson

  2. Rovira i Virgili University, Tarragona, Spain

    Carlos Martín-Vide

  3. University of Extremadura, Cáceres, Spain

    Miguel A. Vega-Rodríguez

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Brito, K.L., Oliveira, A.R., Dias, U., Dias, Z. (2018). Heuristics for the Sorting Signed Permutations by Reversals and Transpositions Problem. In: Jansson, J., Martín-Vide, C., Vega-Rodríguez, M. (eds) Algorithms for Computational Biology. AlCoB 2018. Lecture Notes in Computer Science(), vol 10849. Springer, Cham. https://doi.org/10.1007/978-3-319-91938-6_6

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  • DOI: https://doi.org/10.1007/978-3-319-91938-6_6

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-91937-9

  • Online ISBN: 978-3-319-91938-6

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