Genome Rearrangements and Sorting by Reversals
SIAM Journal on Computing
Efficient algorithms for multichromosomal genome rearrangements
Journal of Computer and System Sciences - Computational biology 2002
Transforming men into mice: the Nadeau-Taylor chromosomal breakage model revisited
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
Edit Distances for Genome Comparisons Based on Non-Local Operations
CPM '92 Proceedings of the Third Annual Symposium on Combinatorial Pattern Matching
Transforming men into mice (polynomial algorithm for genomic distance problem)
FOCS '95 Proceedings of the 36th Annual Symposium on Foundations of Computer Science
Genome rearrangements: a correct algorithm for optimal capping
Information Processing Letters
HP Distance Via Double Cut and Join Distance
CPM '08 Proceedings of the 19th annual symposium on Combinatorial Pattern Matching
A unifying view of genome rearrangements
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Rearrangement Models and Single-Cut Operations
RECOMB-CG '09 Proceedings of the International Workshop on Comparative Genomics
Limited lifespan of fragile regions in mammalian evolution
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
Approximating the number of Double Cut-and-Join scenarios
Theoretical Computer Science
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In the past years, many combinatorial arguments have been made to support the theory that mammalian genome rearrangement scenarios rely heavily on breakpoint reuse. Different models of genome rearrangements have been suggested, from the classical set of operations that include inversions, translocations, fusions and fissions, to more elaborate models that include transpositions. Here we show that the current definition of breakpoint reuse rateis based on assumptions that are seldom true for mammalian genomes, and propose a new approach to compute this parameter. We explore the formal properties of this new measure and apply these results to the human-mouse genome comparison. We show that the reuse rate is intimately linked to a particular rearrangement scenario, and that the reuse rate can vary from 0.89 to 1.51 for scenarios of the same length that transform the mouse genome into the human genome, where a rate of 1 indicates no reuse at all.