Formulations and hardness of multiple sorting by reversals
RECOMB '99 Proceedings of the third annual international conference on Computational molecular biology
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
On the Practical Solution of the Reversal Median Problem
WABI '01 Proceedings of the First International Workshop on Algorithms in Bioinformatics
Finding an Optimal Inversion Median: Experimental Results
WABI '01 Proceedings of the First International Workshop on Algorithms in Bioinformatics
Inversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction from Gene-Order Data
WABI '02 Proceedings of the Second 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
A linear time algorithm for the inversion median problem in circular bacterial genomes
Journal of Discrete Algorithms
A simulation tool for the study of symmetric inversions in bacterial genomes
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
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In the median problem, we are given a distance or dissimilarity measure d, three genomes G1,G2, and G3, and we want to find a genome G (a median) such that the sum ∑$_{i=1}^{\rm 3}$d(G,Gi) is minimized. The median problem is a special case of the multiple genome rearrangement problem, where one wants to find a phylogenetic tree describing the most “plausible” rearrangement scenario for multiple species. The median problem is NP-hard for both the breakpoint and the reversal distance [5,14]. To the best of our knowledge, there is no approach yet that takes biological constraints on genome rearrangements into account. In this paper, we make use of the fact that in circular bacterial genomes the predominant mechanism of rearrangement are inversions that are centered around the origin or the terminus of replication [8,10,18]. This constraint simplifies the median problem significantly. More precisely, we show that the median problem for the reversal distance can be solved in linear time for circular bacterial genomes.