Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals
STOC '95 Proceedings of the twenty-seventh annual ACM symposium on Theory of computing
Finding an Optimal Inversion Median: Experimental Results
WABI '01 Proceedings of the First International Workshop on Algorithms in Bioinformatics
Algorithms for Finding Gene Clusters
WABI '01 Proceedings of the First International Workshop on Algorithms in Bioinformatics
Edit Distances for Genome Comparisons Based on Non-Local Operations
CPM '92 Proceedings of the Third Annual Symposium on Combinatorial Pattern Matching
INFORMS Journal on Computing
Genome Rearrangement Based on Reversals that Preserve Conserved Intervals
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
On the similarity of sets of permutations and its applications to genome comparison
COCOON'03 Proceedings of the 9th annual international conference on Computing and combinatorics
Using PQ trees for comparative genomics
CPM'05 Proceedings of the 16th annual conference on Combinatorial Pattern Matching
Solving the Preserving Reversal Median Problem
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A fast and exact algorithm for the perfect reversal median problem
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
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An important problem for phylogenetic investigations that are based on gene orders is to find for three given gene orders a fourth gene order that has a minimum sum of reversal distances to the three given gene orders. This problem is called Reversal Median problem (RMP). The RMP is studied here under the constraint that common (combinatorial) structures are preserved which are modeled as common intervals. An existing branch-and-bound algorithm for RMP is extended here so that it can solve the RMP with common intervals optimally. This algorithm is applied to mitochondrial gene order data for different animal taxa. It is shown that common intervals occur often for most taxa and that many common intervals are destroyed when the RMP is solved optimally with standard methods that do not consider common intervals.