A general framework for genome rearrangement with biological constraints

Algorithms for Molecular Biology : AMB
Pijus SimonaitisKrister M Swenson

Abstract

This paper generalizes previous studies on genome rearrangement under biological constraints, using double cut and join (DCJ). We propose a model for weighted DCJ, along with a family of optimization problems called φ -MCPS (Minimum Cost Parsimonious Scenario), that are based on labeled graphs. We show how to compute solutions to general instances of φ -MCPS, given an algorithm to compute φ -MCPS on a circular genome with exactly one occurrence of each gene. These general instances can have an arbitrary number of circular and linear chromosomes, and arbitrary gene content. The practicality of the framework is displayed by presenting polynomial-time algorithms that generalize the results of Bulteau, Fertin, and Tannier on the Sorting by wDCJs and indels in intergenes problem, and that generalize previous results on the Minimum Local Parsimonious Scenario problem.

References

Feb 1, 1984·Proceedings of the National Academy of Sciences of the United States of America·J H Nadeau, B A Taylor
Jun 12, 1996·Gene·M BlanchetteD Sankoff
Jun 14, 2005·Bioinformatics·Sophia YancopoulosRichard Friedberg
Jun 15, 2011·BMC Genomics·Amélie S VéronMarie-France Sagot
Dec 24, 2015·BMC Bioinformatics·Christian BaudetZanoni Dias
May 18, 2016·Genome Biology and Evolution·Priscila BillerEric Tannier
May 18, 2016·Algorithms for Molecular Biology : AMB·Krister M SwensonMathieu Blanchette
Feb 12, 2017·BMC Bioinformatics·Laurent BulteauEric Tannier
Jun 8, 2017·BMC Genomics·Nikita Alexeev, Max A Alekseyev
Jun 9, 2017·Algorithms for Molecular Biology : AMB·Guillaume FertinEric Tannier
May 15, 2018·Algorithms for Molecular Biology : AMB·Pijus Simonaitis, Krister M Swenson

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