A Unified ILP Framework for Genome Median, Halving, and Aliquoting Problems Under DCJ

Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10562)


One of the key computational problems in comparative genomics is the reconstruction of genomes of ancestral species based on genomes of extant species. Since most dramatic changes in genomic architectures are caused by genome rearrangements, this problem is often posed as minimization of the number of genome rearrangements between extant and ancestral genomes. The basic case of three given genomes is known as the genome median problem. Whole genome duplications (WGDs) represent yet another type of dramatic evolutionary events and inspire the reconstruction of pre-duplicated ancestral genomes, referred to as the genome halving problem. Generalization of WGDs to whole genome multiplication events leads to the genome aliquoting problem.

In the present study, we provide polynomial-size integer linear programming formulations for the aforementioned problems. We further obtain such formulations for the restricted versions of the median and halving problems, which have been recently introduced for improving biological relevance.


Medical Genomics Genome Median Problem (GMP) Whole Genome Multiplication (WGM) Whole-genome Duplication (WGD) Breakpoint Graph 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



The work of PA and MAA is supported by the National Science Foundation under the grant No. IIS-1462107. The work of NA and YR is partially supported by the National Science Foundation under the grant No. DMS-1406984.


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Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  1. 1.The George Washington UniversityWashington, D.C.USA

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