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Bioinformatics Advance Access originally published online on October 28, 2004
Bioinformatics 2005 21(7):869-879; doi:10.1093/bioinformatics/bti107
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© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Theoretical and practical advances in genome halving

Peng Yin * and Alexander J. Hartemink *

Department of Computer Science, Duke University Box 90129, Durham, NC 27708-0129, USA

*To whom correspondence should be addressed.

Motivation: Duplication of an organism's entire genome is a rare but spectacular event, enabling the rapid emergence of multiple new gene functions. Over time, the parallel linkage of duplicated genes across chromosomes may be disrupted by reciprocal translocations, while the intra-chromosomal order of genes may be shuffled by inversions and transpositions. Some duplicate genes may evolve unrecognizably or be deleted. As a consequence, the only detectable signature of an ancient duplication event in a modern genome may be the presence of various chromosomal segments containing parallel paralogous genes, with each segment appearing exactly twice in the genome. The problem of reconstructing the linkage structure of an ancestral genome before duplication is known as genome halving with unordered chromosomes.

Results: In this paper, we derive a new upper bound on the genome halving distance that is tighter than the best known, and a new lower bound that is almost always tighter than the best known. We also define the notion of genome halving diameter, and obtain both upper and lower bounds for it. Our tighter bounds on genome halving distance yield a new algorithm for reconstructing an ancestral duplicated genome. We create a software package GenomeHalving based on this new algorithm and test it on the yeast genome, identifying a sequence of translocations for halving the yeast genome that is shorter than previously conjectured possible.

Availability: GenomeHalving is available upon email request.

Contact: py{at}cs.duke.edu; amink{at}cs.duke.edu


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