Journal of the ACM (JACM)
Exemplar Longest Common Subsequence
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Comparing Genomes with Duplications: A Computational Complexity Point of View
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
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
Combinatorics of Genome Rearrangements
Combinatorics of Genome Rearrangements
A polynomial algebra method for computing exemplar breakpoint distance
ISBRA'11 Proceedings of the 7th international conference on Bioinformatics research and applications
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
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The exemplar breakpoint distance problem is one of the most important problems in genome comparison and has been extensively studied in the literature. The exemplar breakpoint distance problem cannot be approximated within any factor even if each gene family occurs at most twice in a genome. This is due to the fact that its decision version, the zero exemplar breakpoint distance problem where each gene family occurs at most twice in a genome (ZEBD$((2,2))$ for short) is NP-hard. Thus, the basic version ZEBD$((2,2))$ has attracted the attention of many scientists. The best existing algorithm for ZEBD$((2,2))$ runs in $(O(n2^n))$ time. In this paper, we propose a new algorithm for ZEBD$((2,2))$ with running time $(O(n^2{1.86121^n}))$. We have implemented the algorithm in Java. The software package is available upon request.