Annual Symposium on Combinatorial Pattern Matching

CPM 2015: Combinatorial Pattern Matching pp 396-409

Sorting by Cuts, Joins and Whole Chromosome Duplications

Conference paper

DOI: 10.1007/978-3-319-19929-0_34

Volume 9133 of the book series Lecture Notes in Computer Science (LNCS)
Cite this paper as:
Zeira R., Shamir R. (2015) Sorting by Cuts, Joins and Whole Chromosome Duplications. In: Cicalese F., Porat E., Vaccaro U. (eds) Combinatorial Pattern Matching. CPM 2015. Lecture Notes in Computer Science, vol 9133. Springer, Cham

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 

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  1. 1.Tel-Aviv UniversityTel-AvivIsrael