Sorting by Cuts, Joins and Whole Chromosome Duplications
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.
KeywordsSCJ Genome rearrangements Computational genomics
We thank our referees for many helpful and insightful comments. This study was supported by the Israeli Science Foundation (grant 317/13) and the Dotan Hemato-Oncology Research Center at Tel Aviv University. RZ was supported in part by fellowships from the Edmond J. Safra Center for Bioinformatics at Tel Aviv University and from the Israeli Center of Research Excellence (I-CORE) Gene Regulation in Complex Human Disease (Center No 41/11).
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