A Linear-Time Algorithm for the Copy Number Transformation Problem

Ron Zeira, Meirav Zehavi, Ron Shamir

Research output: Contribution to journalArticlepeer-review

5 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 segment along a chromosome is called its copy number profile (CNP). Understanding CNP changes can assist in predicting disease progression and treatment. To date, questions related to distances between CNPs gained little scientific attention. Here we focus on the following fundamental problem, introduced by Schwarz et al.: given two CNPs, u and v, compute the minimum number of operations transforming u into 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
Pages (from-to)1179-1194
Number of pages16
JournalJournal of Computational Biology
Volume24
Issue number12
DOIs
StatePublished - 1 Dec 2017
Externally publishedYes

Keywords

  • copy number
  • edit distance
  • genome rearrangement

ASJC Scopus subject areas

  • Modeling and Simulation
  • Molecular Biology
  • Genetics
  • Computational Mathematics
  • Computational Theory and Mathematics

Fingerprint

Dive into the research topics of 'A Linear-Time Algorithm for the Copy Number Transformation Problem'. Together they form a unique fingerprint.

Cite this