Sorting by Cuts, Joins and Whole Chromosome Duplications

Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9133)

Abstract

Genome rearrangement problems have been extensively studied due to their importance in biology. Most studied models assumed a single copy per gene. However, in reality duplicated genes are common, most notably in cancer. Here we make a step towards handling duplicated genes by considering a model that allows the atomic operations of cut, join and whole chromosome duplication. Given two linear genomes, \(\varGamma \) with one copy per gene, and \(\varDelta \) with two copies per gene, we give a linear time algorithm for computing a shortest sequence of operations transforming \(\varGamma \) into \(\varDelta \) such that all intermediate genomes are linear. We also show that computing an optimal sequence with fewest duplications is NP-hard.

Keywords

SCJ Genome rearrangements Computational genomics 

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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  1. 1.Tel-Aviv UniversityTel-AvivIsrael

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