Finding local genome rearrangements

Algorithms for Molecular Biology : AMB
Pijus Simonaitis, Krister M Swenson

Abstract

The double cut and join (DCJ) model of genome rearrangement is well studied due to its mathematical simplicity and power to account for the many events that transform gene order. These studies have mostly been devoted to the understanding of minimum length scenarios transforming one genome into another. In this paper we search instead for rearrangement scenarios that minimize the number of rearrangements whose breakpoints are unlikely due to some biological criteria. One such criterion has recently become accessible due to the advent of the Hi-C experiment, facilitating the study of 3D spacial distance between breakpoint regions. We establish a link between the minimum number of unlikely rearrangements required by a scenario and the problem of finding a maximum edge-disjoint cycle packing on a certain transformed version of the adjacency graph. This link leads to a 3/2-approximation as well as an exact integer linear programming formulation for our problem, which we prove to be NP-complete. We also present experimental results on fruit flies, showing that Hi-C data is informative when used as a criterion for rearrangements. A new variant of the weighted DCJ distance problem is addressed that ignores scenario length in its objec...Continue Reading

References

Jun 12, 1996·Gene·M BlanchetteD Sankoff
Jun 17, 2003·Nature Genetics·Jeffrey J RoixTom Misteli
Jul 12, 2003·Bioinformatics·J F LefebvreD Sankoff
Sep 30, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Aïda Ouangraoua, Anne Bergeron
Sep 30, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Marília D V Braga, Jens Stoye
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Jun 15, 2011·BMC Genomics·Amélie S VéronMarie-France Sagot
Jan 14, 2016·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Gustavo Rodrigues GalvaoZanoni Dias
May 18, 2016·Algorithms for Molecular Biology : AMB·Krister M SwensonMathieu Blanchette

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Citations

Jul 31, 2019·Algorithms for Molecular Biology : AMB·Pijus SimonaitisKrister M Swenson
Sep 13, 2019·Bioinformatics·Krister M Swenson, Mathieu Blanchette

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Methods Mentioned

BETA
Hi-C

Software Mentioned

Hi
Orthocluster
MLS

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