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 tanspositions
Proceedings of the sixth annual ACM-SIAM symposium on Discrete algorithms
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Phylogenetic Reconstruction from Arbitrary Gene-Order Data
BIBE '04 Proceedings of the 4th IEEE Symposium on Bioinformatics and Bioengineering
On the tandem duplication-random loss model of genome rearrangement
SODA '06 Proceedings of the seventeenth annual ACM-SIAM symposium on Discrete algorithm
Using median sets for inferring phylogenetic trees
Bioinformatics
Approximating the true evolutionary distance between two genomes
Journal of Experimental Algorithmics (JEA)
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A variant of the tandem duplication — random loss model of genome rearrangement
Theoretical Computer Science
Finding All Sorting Tandem Duplication Random Loss Operations
CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
Parking Functions, Labeled Trees and DCJ Sorting Scenarios
RECOMB-CG '09 Proceedings of the International Workshop on Comparative Genomics
Approximating the number of Double Cut-and-Join scenarios
Theoretical Computer Science
Tandem halving problems by DCJ
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
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A tandem duplication random loss (TDRL) operation duplicates a contiguous segment of genes, followed by the random loss of one copy of each of the duplicated genes. Although the importance of this operation is founded by several recent biological studies, it has been investigated only rarely from a theoretical point of view. Of particular interest are sorting TDRLs which are TDRLs that, when applied to a permutation representing a genome, reduce the distance towards another given permutation. The identification of sorting genome rearrangement operations in general is a key ingredient of many algorithms for reconstructing the evolutionary history of a set of species. In this paper we present methods to compute all sorting TDRLs for two given gene orders. In addition, a closed formula for the number of sorting TDRLs is derived and further properties of sorting TDRLs are investigated. It is also shown that the theoretical findings are useful for identifying unique sorting TDRL scenarios for mitochondrial gene orders.