Sorting by cuts, joins and whole chromosome duplications

Ron Zeira, Ron Shamir

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review


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, Γ with one copy per gene, and Δ with two copies per gene, we give a linear time algorithm for computing a shortest sequence of operations transforming Γ into Δ such that all intermediate genomes are linear. We also show that computing an optimal sequence with fewest duplications is NP-hard.

Original languageEnglish
Title of host publicationCombinatorial Pattern Matching - 26th Annual Symposium, CPM 2015, Proceedings
EditorsUgo Vaccaro, Ely Porat, Ferdinando Cicalese
PublisherSpringer Verlag
Number of pages14
ISBN (Print)9783319199283
StatePublished - 2015
Event26th Annual Symposium on Combinatorial Pattern Matching, CPM 2015 - Ischia Island, Italy
Duration: 29 Jun 20151 Jul 2015

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Conference26th Annual Symposium on Combinatorial Pattern Matching, CPM 2015
CityIschia Island


  • Computational genomics
  • Genome rearrangements
  • SCJ


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