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Bioinformatics Vol. 19 Suppl. 1 2003
Pages i190-i196
© 2003 Oxford University Press

Detection and validation of single gene inversions

J.F. Lefebvre 1, N. El-Mabrouk 1, E. Tillier 2 and D. Sankoff 3,*

1 Département d’informatique et recherche opérationnelle, Université de Montréal, CP 6128 succ. Centre-ville, Montréal, Québec H3C 3J7, Canada
2 Ontario Cancer Institute, Princess Margaret Hospital, 620 University Avenue, Suite 703, Toronto, Canada
3 Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa K1N 6N5, Canada

Received on January 6, 2003 ; accepted on February 20, 2003

Motivation: The biologically meaningful algorithmic study of genome rearrangement should take into account the distribution of sizes of the rearranged genomic fragments. In particular, it is important to know the prevalence of short inversions in order to understand the patterns of gene order disruption observed in comparative genomics.

Results: We find a large excess of short inversions, especially those involving a single gene, in comparison with a random inversion model. This is demonstrated through comparison of four pairs of bacterial genomes, using a specially-designed implementation of the Hannenhalli–Pevzner theory, and validated through experimentation on pairs of random genomes matched to the real pairs.

Availability: The main routines of the experimental software are available through consultation with the authors.

Contact: sankoff{at}uottawa.ca

Keywords: short inversions, reversals, genome rearrangement, genome evolution, comparative genomics, bacterial genomes, Hannenhalli--Pevzner algorithm, experimental algorithmics.

* To whom correspondence should be addressed.


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