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
Sorting permutations by block-interchanges
Information Processing Letters
Polynomial-time algorithm for computing translocation distance between genomes
Discrete Applied Mathematics - Special volume on computational molecular biology
SIAM Journal on Discrete Mathematics
INFORMS Journal on Computing
A 1.375-Approximation Algorithm for Sorting by Transpositions
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Colored de Bruijn Graphs and the Genome Halving Problem
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Sorting by Block-Interchanges and Signed Reversals
ITNG '07 Proceedings of the International Conference on Information Technology
Bioinformatics
A unifying view of genome rearrangements
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Rearrangement Models and Single-Cut Operations
RECOMB-CG '09 Proceedings of the International Workshop on Comparative Genomics
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
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The breakpoint distance is one of the most straightforward genome comparison measures. Surprisingly, when it comes to define it precisely for multichromosomal genomes with both linear and circular chromosomes, there is more than one way to go about it. In this paper we study Single-Cut-or-Join (SCJ), a breakpoint-like rearrangement event for which we present linear and polynomial time algorithms that solve several genome rearrangement problems, such as median and halving. For the multichromosomal linear genome median problem, this is the first polynomial time algorithm described, since for other breakpoint distances this problem is NP-hard. These new results may be of value as a speedily computable, first approximation to distances or phylogenies based on more realistic rearrangement models.