Genome aliquoting with double cut and join.
BACKGROUND
The genome aliquoting problem 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' plus sign in circle B' plus sign in circle ... plus sign in circle B') necessary to convert the observed genome B' plus sign in circle B' plus sign in circle ... plus sign in circle B' into A.


RESULTS
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.


CONCLUSIONS
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.
Warren
Robert
R
School of Information Technology and Engineering, University of Ottawa, 800 King Edward Avenue, Ottawa, Canada. rwarr059@uottawa.ca
Sankoff
David
D
D000465:Algorithms; D000818:Animals; D002874:Chromosome Mapping / Q000379:methods; D016678:Genome; D006801:Humans