A linear-time algorithm for the copy number transformation problem

Ron Shamir, Meirav Zehavi, Ron Zeira

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

8 Scopus citations

Abstract

Problems of genome rearrangement are central in both evolution and cancer. Most evolutionary scenarios have been studied under the assumption that the genome contains a single copy of each gene. In contrast, tumor genomes undergo deletions and duplications, and thus the number of copies of genes varies. The number of copies of each gene along a chromosome is called its copy number profile. Understanding copy number profile changes can assist in predicting disease progression and treatment. To date, questions related to distances between copy number profiles gained little scientific attention. Here we focus on the following fundamental problem, introduced by Schwarz et al. (PLOS Comp. Biol., 2014): given two copy number profiles, u and v, compute the edit distance from u to v, where the edit operations are segmental deletions and amplifications. We establish the computational complexity of this problem, showing that it is solvable in linear time and constant space.

Original languageEnglish
Title of host publication27th Annual Symposium on Combinatorial Pattern Matching, CPM 2016
EditorsRoberto Grossi, Moshe Lewenstein
PublisherSchloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing
Pages16.1-16.13
ISBN (Electronic)9783959770125
DOIs
StatePublished - 1 Jun 2016
Externally publishedYes
Event27th Annual Symposium on Combinatorial Pattern Matching, CPM 2016 - Tel Aviv, Israel
Duration: 27 Jun 201629 Jun 2016

Publication series

NameLeibniz International Proceedings in Informatics, LIPIcs
Volume54
ISSN (Print)1868-8969

Conference

Conference27th Annual Symposium on Combinatorial Pattern Matching, CPM 2016
Country/TerritoryIsrael
CityTel Aviv
Period27/06/1629/06/16

Keywords

  • Copy number
  • Genome rearrangement

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