TY - GEN
T1 - A linear-time algorithm for the copy number transformation problem
AU - Shamir, Ron
AU - Zehavi, Meirav
AU - Zeira, Ron
N1 - Publisher Copyright:
© Ron Shamir, Meirav Zehavi, and Ron Zeira.
PY - 2016/6/1
Y1 - 2016/6/1
N2 - 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.
AB - 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.
KW - Copy number
KW - Genome rearrangement
UR - http://www.scopus.com/inward/record.url?scp=85011948991&partnerID=8YFLogxK
U2 - 10.4230/LIPIcs.CPM.2016.16
DO - 10.4230/LIPIcs.CPM.2016.16
M3 - Conference contribution
AN - SCOPUS:85011948991
T3 - Leibniz International Proceedings in Informatics, LIPIcs
SP - 16.1-16.13
BT - 27th Annual Symposium on Combinatorial Pattern Matching, CPM 2016
A2 - Grossi, Roberto
A2 - Lewenstein, Moshe
PB - Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing
T2 - 27th Annual Symposium on Combinatorial Pattern Matching, CPM 2016
Y2 - 27 June 2016 through 29 June 2016
ER -