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
Efficient algorithms for multichromosomal genome rearrangements
Journal of Computer and System Sciences - Computational biology 2002
Transforming men into mice (polynomial algorithm for genomic distance problem)
FOCS '95 Proceedings of the 36th Annual Symposium on Foundations of Computer Science
Ant Colony Optimization
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)
An improved ant colony optimisation heuristic for graph colouring
Discrete Applied Mathematics
An efficient probabilistic population-based descent for the median genome problem
Proceedings of the 10th annual conference on Genetic and evolutionary computation
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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A genome rearrangement scenario describes a series of chromosome fusion, fission, and translocation operations that suffice to rewrite one genome into another. Exact algorithmic methods for this important problem focus on providing one solution, while the set of distance-wise equivalent scenarios is very large. Moreover, no criteria for filtering for biologically plausible scenarios is currently proposed. We present an original metaheuristic method that uses Ant Colony Optimization to randomly explore the space of optimal and suboptimal rearrangement scenarios. It improves on the state of the art both by permitting large-scale enumeration of optimal scenarios, and by labeling each with metrics that can be used for post-processing filtering based on biological constraints.