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
Theoretical Computer Science - Special papers from: COCOON 2003
On the tandem duplication-random loss model of genome rearrangement
SODA '06 Proceedings of the seventeenth annual ACM-SIAM symposium on Discrete algorithm
Spectrum of Sizes for Perfect Deletion-Correcting Codes
SIAM Journal on Discrete Mathematics
Conserved interval distance computation between non-trivial genomes
COCOON'05 Proceedings of the 11th annual international conference on Computing and Combinatorics
A parallel implementation for determining genomic distances under deletion and insertion
ICCS'05 Proceedings of the 5th international conference on Computational Science - Volume Part II
Calculating genomic distances in parallel using OpenMP
Transactions on Computational Systems Biology II
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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 multi-set 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 and 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.