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 by reversals is difficult
RECOMB '97 Proceedings of the first annual international conference on Computational molecular biology
Formulations and hardness of multiple sorting by reversals
RECOMB '99 Proceedings of the third annual international conference on Computational molecular biology
Inversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction from Gene-Order Data
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Genomic distances under deletions and insertions
COCOON'03 Proceedings of the 9th annual international conference on Computing and combinatorics
Comparing Genomes with Duplications: A Computational Complexity Point of View
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Approximating the true evolutionary distance between two genomes
Journal of Experimental Algorithmics (JEA)
Sorting Genomes with Insertions, Deletions and Duplications by DCJ
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
Approximability and Fixed-Parameter Tractability for the Exemplar Genomic Distance Problems
TAMC '09 Proceedings of the 6th Annual Conference on Theory and Applications of Models of Computation
RECOMB-CG'07 Proceedings of the 2007 international conference on Comparative genomics
A heuristic algorithm for reconstructing ancestral gene orders with duplications
RECOMB-CG'07 Proceedings of the 2007 international conference on Comparative genomics
On the approximability of comparing genomes with duplicates
WALCOM'08 Proceedings of the 2nd international conference on Algorithms and computation
Efficient algorithms for analyzing segmental duplications, deletions, and inversions in genomes
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
Bootstrapping phylogenies inferred from rearrangement data
WABI'11 Proceedings of the 11th international conference on Algorithms in bioinformatics
Maximizing synteny blocks to identify ancestral homologs
RCG'05 Proceedings of the 2005 international conference on Comparative Genomics
A framework for orthology assignment from gene rearrangement data
RCG'05 Proceedings of the 2005 international conference on Comparative Genomics
The approximability of the exemplar breakpoint distance problem
AAIM'06 Proceedings of the Second international conference on Algorithmic Aspects in Information and Management
Lower bounds on the approximation of the exemplar conserved interval distance problem of genomes
COCOON'06 Proceedings of the 12th annual international conference on Computing and Combinatorics
A parsimony approach to genome-wide ortholog assignment
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
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As more and more genomes are sequenced, evolutionary biologists are becoming increasingly interested in evolution at the level of whole genomes, in scenarios in which the genome evolves through insertions, deletions, and movements of genes along its chromosomes. In the mathematical model pioneered by Sankoff and others, a unichromosomal genome is represented by a signed permutation of a multiset of genes; Hannenhalli and Pevzner showed that the edit distance between two signed permutations of the same set can be computed in polynomial time when all operations are inversions. El-Mabrouk extended that result to allow deletions (or conversely, a limited form of insertions which forbids duplications). In this paper, we extend El-Mabrouk's work to handle duplications as well as insertions and present an alternate framework for computing (near) minimal edit sequences involving insertions, deletions, and inversions. We derive an error bound for our polynomial-time distance computation under various assumptions and present preliminary experimental results that suggest that performance in practice may be excellent, within a few percent of the actual distance.