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 All Common Intervals of k Permutations
CPM '01 Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching
An algorithmic view of gene teams
Theoretical Computer Science
Advances on sorting by reversals
Discrete Applied Mathematics
Perfect Sorting by Reversals Is Not Always Difficult
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Evolution under Reversals: Parsimony and Conservation of Common Intervals
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
Ultra-perfect sorting scenarios
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
Perfect sorting by reversals is not always difficult
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
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In computational biology, gene order data is often modelled as signed permutations. A classical problem in genome comparison is to detect conserved segments in a permutation, that is, genes that are co-localised in several species, indicating that they remained grouped during evolution. A second largely studied problem related to gene order data is to compute a minimum scenario of reversals that transforms a signed permutation into another. Several studies began to mix the two problems, and it was observed that their results are not always compatible: often parsimonious scenarios of reversals break conserved segments. In a recent study, Bérard, Bergeron and Chauve stated as an open question whether it was possible to design a polynomial time algorithm to decide if there exists a minimum scenario of reversals that transforms a genome into another while keeping the clusters of co-localised genes together. In this paper, we give this polynomial algorithm, and thus generalise the theoretical result of the aforementioned paper.