Computers and Intractability: A Guide to the Theory of NP-Completeness
Computers and Intractability: A Guide to the Theory of NP-Completeness
CPM '96 Proceedings of the 7th Annual Symposium on Combinatorial Pattern Matching
Exemplar Longest Common Subsequence
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
The ExemplarBreakpointDistance for Non-trivial Genomes Cannot Be Approximated
WALCOM '09 Proceedings of the 3rd International Workshop on Algorithms and Computation
Repetition-free longest common subsequence
Discrete Applied Mathematics
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
Parameterized Complexity
A polynomial algebra method for computing exemplar breakpoint distance
ISBRA'11 Proceedings of the 7th international conference on Bioinformatics research and applications
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)
Evolution of genome organization by duplication and loss: an alignment approach
RECOMB'12 Proceedings of the 16th Annual international conference on Research in Computational Molecular Biology
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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Given two genomes with duplicate genes, ZERO EXEMPLAR DISTANCE is the problem of deciding whether the two genomes can be reduced to the same genome without duplicate genes by deleting all but one copy of each gene in each genome. Blin, Fertin, Sikora, and Vialette recently proved that ZERO EXEMPLAR DISTANCE for monochromosomal genomes is NP-hard even if each gene appears at most two times in each genome, thereby settling an important open question on genome rearrangement in the exemplar model. In this paper, we give a very simple alternative proof of this result. We also study the problem ZERO EXEMPLAR DISTANCE for multichromosomal genomes without gene order: from one direction, we show that this problem is NP-hard even if each gene appears at most two times in each genome; from the other direction, we show that this problem admits a polynomial-time algorithm if only one of the two genomes has duplicate genes, and is fixed-parameter tractable if the parameter is the maximum number of chromosomes in each genome.