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A 1.375-Approximation Algorithm for Sorting by Transpositions with Faster Running Time

Published: 16 December 2022 Publication History

Abstract

Sorting Permutations by Transpositions is a famous problem in the Computational Biology field. This problem is NP-Hard, and the best approximation algorithm, proposed by Elias and Hartman in 2006, has an approximation factor of 1.375. Since then, several researchers have proposed modifications to this algorithm to reduce the time complexity. More recently, researchers showed that the algorithm proposed by Elias and Hartman might need one more operation above the approximation ratio and presented a new 1.375-approximation algorithm using an algebraic approach that corrected this issue. This algorithm runs in time. In this paper, we present an efficient way to fix Elias and Hartman algorithm that runs in . By comparing the three approximation algorithms with all permutations of size, we also show that our algorithm finds the exact distance in more instances than the previous two algorithms.

References

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Christie, D.A.: Genome Rearrangement Problems. Ph.D. thesis, Department of Computing Science, University of Glasgow (1998)
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Dias, U., Dias, Z.: An improved -approximation algorithm for the transposition distance problem. In: Proceeding of the 1st ACM International Conference on Bioinformatics and Computational Biology (BCB’2010), pp. 334–337. ACM, New York (2010)
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Dias, U., Dias, Z.: Extending bafna-pevzner algorithm. In: Proceedings of the 1st International Symposium on Biocomputing (ISB’2010), pp. 1–8. ACM, New York (2010)
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Dias, U.M.: Problemas de Comparação de Genomas. Ph.D. thesis, Institute of Computing, University of Campinas (2012). In Portuguese
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Elias I and Hartman T A 1.375-approximation algorithm for sorting by transpositions IEEE ACM Trans. Comput. Biol. Bioinf. 2006 3 4 369-379
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Silva LAG, Kowada LAB, Rocco NR, and Walter MEMT A new 1.375-approximation algorithm for sorting by transpositions Algorithms Mol. Biol. 2022 17 1 1-17
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Walter, M.E.M.T., Dias, Z., Meidanis, J.: A new approach for approximating the transposition distance. In: Titsworth, F.M. (ed.) Proceedings of the 7th String Processing and Information Retrieval (SPIRE’2000), pp. 199–208. IEEE Computer Society, Los Alamitos (2000)

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Published In

cover image Guide Proceedings
Advances in Bioinformatics and Computational Biology: 15th Brazilian Symposium on Bioinformatics, BSB 2022, Buzios, Brazil, September 21–23, 2022, Proceedings
Sep 2022
176 pages
ISBN:978-3-031-21174-4
DOI:10.1007/978-3-031-21175-1

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Springer-Verlag

Berlin, Heidelberg

Publication History

Published: 16 December 2022

Author Tags

  1. Genome rearrangements
  2. Transpositions
  3. Time complexity analysis

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