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This article is part of the supplement: Selected papers from the Seventh Asia-Pacific Bioinformatics Conference (APBC 2009)

Open Access Open Badges Research

Genome aliquoting with double cut and join

Robert Warren1 and David Sankoff2

Author Affiliations

1 School of Information Technology and Engineering, University of Ottawa, 800 King Edward Avenue, Ottawa, Canada

2 Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Canada

BMC Bioinformatics 2009, 10(Suppl 1):S2  doi:10.1186/1471-2105-10-S1-S2

Published: 30 January 2009



The genome aliquoting probem is, given an observed genome A with n copies of each gene, presumed to descend from an n-way polyploidization event from an ordinary diploid genome B, followed by a history of chromosomal rearrangements, to reconstruct the identity of the original genome B'. The idea is to construct B', containing exactly one copy of each gene, so as to minimize the number of rearrangements d(A, B' B' ⊕ ... ⊕ B') necessary to convert the observed genome B' B' ⊕ ... ⊕ B' into A.


In this paper we make the first attempt to define and solve the genome aliquoting problem. We present a heuristic algorithm for the problem as well the data from our experiments demonstrating its validity.


The heuristic performs well, consistently giving a non-trivial result. The question as to the existence or non-existence of an exact solution to this problem remains open.