Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals
Journal of the ACM (JACM)
Linear FPT reductions and computational lower bounds
STOC '04 Proceedings of the thirty-sixth annual ACM symposium on Theory of computing
Mathematics of Evolution and Phylogeny
Mathematics of Evolution and Phylogeny
The approximability of the exemplar breakpoint distance problem
AAIM'06 Proceedings of the Second international conference on Algorithmic Aspects in Information and Management
Conserved interval distance computation between non-trivial genomes
COCOON'05 Proceedings of the 11th annual international conference on Computing and Combinatorics
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
Genomes containing duplicates are hard to compare
ICCS'06 Proceedings of the 6th international conference on Computational Science - Volume Part II
Parameterized Complexity
On Recovering Syntenic Blocks from Comparative Maps
COCOA 2008 Proceedings of the 2nd international conference on Combinatorial Optimization and Applications
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
On the approximability of comparing genomes with duplicates
WALCOM'08 Proceedings of the 2nd international conference on Algorithms and computation
Filling scaffolds with gene repetitions: maximizing the number of adjacencies
CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
Scaffold Filling under the Breakpoint and Related Distances
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
An Improved Approximation Algorithm for Scaffold Filling to Maximize the Common Adjacencies
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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In this paper we define a new similarity measure, the nonbreaking similarity, which is the complement of the famous breakpoint distance between genomes (in general, between any two sequences drawn from the same alphabet). When the two input genomes G and H, drawn from the same set of n gene families, contain gene repetitions, we consider the corresponding Exemplar Non-breaking Similarity problem (ENbS) in which we need to delete repeated genes in G and H such that the resulting genomes G and H have the maximum non-breaking similarity. We have the following results. - For the Exemplar Non-breaking Similarity problem, we prove that the Independent Set problem can be linearly reduced to this problem. Hence, ENbS does not admit any factor-n1-ε polynomial-time approximation unless P=NP. (Also, ENbS is W[1]-complete.) - We show that for several practically interesting cases of the Exemplar Non-breaking Similarity problem, there are polynomial time algorithms.