Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals
Journal of the ACM (JACM)
A Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals
SIAM Journal on Computing
Efficient and practical algorithms for sequential modular decomposition
Journal of Algorithms
Finding All Common Intervals of k Permutations
CPM '01 Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching
Edit Distances for Genome Comparisons Based on Non-Local Operations
CPM '92 Proceedings of the Third Annual Symposium on Combinatorial Pattern Matching
Sorting signed permutations by reversals, revisited
Journal of Computer and System Sciences - Special issue on bioinformatics II
Advances on sorting by reversals
Discrete Applied Mathematics
Computing common intervals of K permutations, with applications to modular decomposition of graphs
ESA'05 Proceedings of the 13th annual European conference on Algorithms
COCOON'05 Proceedings of the 11th annual international conference on Computing and Combinatorics
Revisiting t. uno and m. yagiura's algorithm
ISAAC'05 Proceedings of the 16th international conference on Algorithms and Computation
Using PQ trees for comparative genomics
CPM'05 Proceedings of the 16th annual conference on Combinatorial Pattern Matching
RCG'06 Proceedings of the RECOMB 2006 international conference on Comparative Genomics
Conservation of combinatorial structures in evolution scenarios
RCG'04 Proceedings of the 2004 RECOMB international conference on Comparative Genomics
A more efficient algorithm for perfect sorting by reversals
Information Processing Letters
An Algorithm for Inferring Mitogenome Rearrangements in a Phylogenetic Tree
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
Solving the Preserving Reversal Median Problem
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A variant of the tandem duplication — random loss model of genome rearrangement
Theoretical Computer Science
Swarming along the evolutionary branches sheds light on genome rearrangement scenarios
Proceedings of the 11th Annual conference on Genetic and evolutionary computation
Average-Case Analysis of Perfect Sorting by Reversals
CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
Parking Functions, Labeled Trees and DCJ Sorting Scenarios
RECOMB-CG '09 Proceedings of the International Workshop on Comparative Genomics
The solution space of sorting by reversals
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
A fast and exact algorithm for the perfect reversal median problem
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
Posets and permutations in the duplication-loss model: Minimal permutations with d descents
Theoretical Computer Science
Whole mirror duplication-random loss model and pattern avoiding permutations
Information Processing Letters
Minimal permutations with d descents
European Journal of Combinatorics
Ultra-perfect sorting scenarios
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
Survey: A survey of the algorithmic aspects of modular decomposition
Computer Science Review
Longest common separable pattern among permutations
CPM'07 Proceedings of the 18th annual conference on Combinatorial Pattern Matching
Preserving inversion phylogeny reconstruction
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
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We propose new algorithms for computing pairwise rearrangement scenarios that conserve the combinatorial structure of genomes. More precisely, we investigate the problem of sorting signed permutations by reversals without breaking common intervals. We describe a combinatorial framework for this problem that allows us to characterize classes of signed permutations for which one can compute, in polynomial time, a shortest reversal scenario that conserves all common intervals. In particular, we define a class of permutations for which this computation can be done in linear time with a very simple algorithm that does not rely on the classical Hannenhalli-Pevzner theory for sorting by reversals. We apply these methods to the computation of rearrangement scenarios between permutations obtained from 16 synteny blocks of the X chromosomes of the human, mouse, and rat.