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Algorithms for Computing the Family-Free Genomic Similarity Under DCJ

  • Diego P. Rubert
  • Gabriel L. Medeiros
  • Edna A. Hoshino
  • Marília D. V. Braga
  • Jens Stoye
  • Fábio V. MartinezEmail author
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10562)

Abstract

The genomic similarity is a large-scale measure for comparing two given genomes. In this work we study the (NP-hard) problem of computing the genomic similarity under the DCJ model in a setting that does not assume that the genes of the compared genomes are grouped into gene families. This problem is called family-free DCJ similarity. Here we propose an exact ILP algorithm to solve it, we show its APX-hardness, and we present three combinatorial heuristics, with computational experiments comparing their results to the ILP. Experiments on simulated datasets show that the proposed heuristics are very fast and even competitive with respect to the ILP algorithm for some instances.

Keywords

Genome rearrangement Double-cut-and-join Family-free genomic similarity 

Notes

Acknowledgments

We would like to thank Pedro Feijão and Daniel Doerr for helping us with hints on how to get the simulated data for our experiments.

Supplementary material

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Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  • Diego P. Rubert
    • 1
  • Gabriel L. Medeiros
    • 1
  • Edna A. Hoshino
    • 1
  • Marília D. V. Braga
    • 2
  • Jens Stoye
    • 2
  • Fábio V. Martinez
    • 1
    Email author
  1. 1.Faculdade de ComputaçãoUniversidade Federal de Mato Grosso do SulCampo GrandeBrazil
  2. 2.Faculty of Technology and Center for Biotechnology (CeBiTec)Bielefeld UniversityBielefeldGermany

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