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
An algorithm to enumerate all sorting reversals
Proceedings of the sixth annual international conference on Computational biology
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
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
An efficient probabilistic population-based descent for the median genome problem
Proceedings of the 10th annual conference on Genetic and evolutionary computation
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
Improving inversion median computation using commuting reversals and cycle information
RECOMB-CG'07 Proceedings of the 2007 international conference on Comparative genomics
A parallel algorithm for solving the reversal median problem
PPAM'05 Proceedings of the 6th international conference on Parallel Processing and Applied Mathematics
The reversal median problem, common intervals, and mitochondrial gene orders
CompLife'06 Proceedings of the Second international conference on Computational Life Sciences
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The order of genes in the genomes of species can change during evolution and can provide information about their phylogenetic relationship. An interesting method to infer the phylogenetic relationship from the gene orders is to use different types of rearrangement operations and to find possible rearrangement scenarios using these operations. One of the most common rearrangement operations is reversals, which reverse the order of a subset of neighbored genes. In this paper, we study the problem to find the ancestral gene order for three species represented by their gene orders. The rearrangement scenario should use a minimal number of reversals and no other rearrangement operations. This problem is called the Median problem and is known to be NP--complete. In this paper, we describe a heuristic algorithm for finding solutions to the Median problem that searches for rearrangement scenarios with the additional property that gene groups should not be destroyed by reversal operations. The concept of conserved intervals for signed permutations is used to describe such gene groups. We show experimentally, for different types of test problems, that the proposed algorithm produces very good results compared to other algorithms for the Median problem. We also integrate our reversal selection procedure into the well-known MGR and GRAPPA algorithms and show that they achieve a significant speedup while obtaining solutions of the same quality as the original algorithms on the test problems.