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
Faster and simpler algorithm for sorting signed permutations by reversals
SODA '97 Proceedings of the eighth annual ACM-SIAM symposium on Discrete algorithms
CPM '96 Proceedings of the 7th Annual Symposium on Combinatorial Pattern Matching
Transforming men into mice (polynomial algorithm for genomic distance problem)
FOCS '95 Proceedings of the 36th Annual Symposium on Foundations of Computer Science
Inversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction from Gene-Order Data
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Finding All Sorting Tandem Duplication Random Loss Operations
CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
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
Linear programming for phylogenetic reconstruction based on gene rearrangements
CPM'05 Proceedings of the 16th annual conference on Combinatorial Pattern Matching
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
Evolution of tandemly repeated sequences through duplication and inversion
RCG'06 Proceedings of the RECOMB 2006 international conference on Comparative Genomics
Calculating genomic distances in parallel using OpenMP
Transactions on Computational Systems Biology II
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Analysis of genome rearrangements allows to compare molecular data from species that diverged a very long time ago. Results and complexities are tightly related to the type of data and genome-level mutations considered. For sorted and signed data, Hannenhalli and Pevzner (HP) developed the first polynomial algorithm in the field. This algorithm solves the problem of sorting by reversals. In this paper, we show how to extend the HP approach to include insertions and deletions of gene segments, allowing to compare genomes containing different genes. We provide an exact algorithm for the asymmetric case, as applies in or-ganellar genome evolution, and a heuristic for the symmetric case, with bounds and a diagnostic for determining whether the output is optimal.