The complexity of satisfiability problems
STOC '78 Proceedings of the tenth annual ACM symposium on Theory of computing
On the computational complexity of 2-interval pattern matching problems
Theoretical Computer Science
Linear FPT reductions and computational lower bounds
STOC '04 Proceedings of the thirty-sixth annual ACM symposium on Theory of computing
SIAM Journal on Computing
Extracting constrained 2-interval subsets in 2-interval sets
Theoretical Computer Science
Removing Noise and Ambiguities from Comparative Maps in Rearrangement Analysis
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Improved Approximation Algorithms for Predicting RNA Secondary Structures with Arbitrary Pseudoknots
AAIM '07 Proceedings of the 3rd international conference on Algorithmic Aspects in Information and Management
A PTAS for the weighted 2-interval pattern problem over the preceding-and-crossing model
COCOA'07 Proceedings of the 1st international conference on Combinatorial optimization and applications
Approximating the 2-interval pattern problem
ESA'05 Proceedings of the 13th annual European conference on Algorithms
Algorithms for the extraction of synteny blocks from comparative maps
WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
Non-breaking similarity of genomes with gene repetitions
CPM'07 Proceedings of the 18th annual conference on Combinatorial Pattern Matching
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 Tractability of Maximal Strip Recovery
TAMC '09 Proceedings of the 6th Annual Conference on Theory and Applications of Models of Computation
Inapproximability of Maximal Strip Recovery
ISAAC '09 Proceedings of the 20th International Symposium on Algorithms and Computation
Maximal Strip Recovery Problem with Gaps: Hardness and Approximation Algorithms
ISAAC '09 Proceedings of the 20th International Symposium on Algorithms and Computation
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A genomic map is represented by a sequence of gene markers, and a gene marker can appear in several different genomic maps, in either positive or negative form. A strip(syntenic block) is a sequence of distinct markers that appears as subsequences in two or more maps, either directly or in reversed and negated form. Given two genomic maps Gand H, the problem Maximal Strip Recovery(MSR) is to find two subsequences G驴 and H驴 of Gand H, respectively, such that the total length of disjoint strips in G驴 and H驴 is maximized. Previously only a heuristic was provided for this problem, which does not guarantee finding the optimal solution, and it was unknown whether the problem is NP-complete or polynomially solvable. In this paper, we develop a factor-4 polynomial-time approximation algorithm for the problem, and show that several close variants of the problem are intractable.