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A 3.5-Approximation Algorithm for Sorting by Intergenic Transpositions

  • Andre Rodrigues OliveiraEmail author
  • Géraldine Jean
  • Guillaume Fertin
  • Klairton Lima Brito
  • Ulisses Dias
  • Zanoni Dias
Conference paper
  • 34 Downloads
Part of the Lecture Notes in Computer Science book series (LNCS, volume 12099)

Abstract

Genome Rearrangements affect large stretches of genomes during evolution. One of the most studied genome rearrangement is the transposition, which occurs when a sequence of genes is moved to another position inside the genome. Mathematical models have been used to estimate the evolutionary distance between two different genomes based on genome rearrangements. However, many of these models have focused only on the (order of the) genes of a genome, disregarding other important elements in it. Recently, researchers have shown that considering existing regions between each pair of genes, called intergenic regions, can enhance the distance estimation in realistic data. In this work, we study the transposition distance between two genomes, but we also consider intergenic regions, a problem we name Sorting Permutations by Intergenic Transpositions (SbIT). We show that this problem is NP-hard and propose a 3.5-approximation algorithm for it.

Keywords

Genome rearrangements Intergenic regions Transpositions Approximation algorithm 

Notes

Acknowledgments

This work was supported by the National Council for Scientific and Technological Development - CNPq (grants 400487/2016-0, 425340/2016-3, and 140466/2018-5), the São Paulo Research Foundation - FAPESP (grants 2013/08293-7, 2015/11937-9, 2017/12646-3, and 2017/16246-0), the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES) - Finance Code 001, and the CAPES/COFECUB program (grant 831/15).

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Copyright information

© Springer Nature Switzerland AG 2020

Authors and Affiliations

  1. 1.Institute of ComputingUniversity of CampinasCampinasBrazil
  2. 2.LS2N, UMR CNRS 6004, University of NantesNantesFrance
  3. 3.School of TechnologyUniversity of CampinasLimeiraBrazil

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