Finding an Optimal Inversion Median: Experimental Results
WABI '01 Proceedings of the First International Workshop on Algorithms in Bioinformatics
Finding All Common Intervals of k Permutations
CPM '01 Proceedings of the 12th 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
Conservation of combinatorial structures in evolution scenarios
RCG'04 Proceedings of the 2004 RECOMB international conference on Comparative Genomics
Software note: Gene teams: a new formalization of gene clusters for comparative genomics
Computational Biology and Chemistry
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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We present a new algorithm called rEvoluzer II for solving the Reversal Median problem (RMP). Similar to its predecessor rEvoluzer I the new algorithm can preserve conserved intervals but it has the additional property that it is suitable for parallelization. For the parallel version of rEvoluzer II a master-slave parallelization scheme is used and several methods for reducing parallelization overheads have been incorporated. We show experimentally that rEvoluzer achieves very good results compared to other methods for the RMP. It is also shown that the parallel version has good scaling behavior for a not too large number of processors.