SIAM Journal on Computing
Removing Noise and Ambiguities from Comparative Maps in Rearrangement Analysis
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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
Inapproximability of maximal strip recovery: II
FAW'10 Proceedings of the 4th international conference on Frontiers in algorithmics
Algorithms for the extraction of synteny blocks from comparative maps
WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
Parameterized Complexity
Tractability and approximability of maximal strip recovery
CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
An improved approximation algorithm for the complementary maximal strip recovery problem
FAW-AAIM'11 Proceedings of the 5th joint international frontiers in algorithmics, and 7th international conference on Algorithmic aspects in information and management
An improved approximation algorithm for the complementary maximal strip recovery problem
Journal of Computer and System Sciences
Tractability and approximability of maximal strip recovery
Theoretical Computer Science
A linear kernel for the complementary maximal strip recovery problem
CPM'12 Proceedings of the 23rd Annual conference on Combinatorial Pattern Matching
Maximal strip recovery problem with gaps: Hardness and approximation algorithms
Journal of Discrete Algorithms
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Given two genomic maps G 1 and G 2 each represented as a sequence of n gene markers, the maximal strip recovery (MSR) problem is to retain the maximum number of markers in both G 1 and G 2 such that the resultant subsequences, denoted as $G_{1}^{*}$ and $G_{2}^{*}$ , can be partitioned into the same set of maximal substrings of length greater than or equal to two. Such substrings can occur in the reversal and negated form. The complementary maximal strip recovery (CMSR) problem is to delete the minimum number of markers from both G 1 and G 2 for the same purpose, with its optimization goal exactly complementary to maximizing the total number of gene markers retained in the final maximal substrings. Both MSR and CMSR have been shown NP-hard and APX-hard. A 4-approximation algorithm is known for the MSR problem, but no constant ratio approximation algorithm for CMSR. In this paper, we present an O(3 k n 2)-time fixed-parameter tractable (FPT) algorithm, where k is the size of the optimal solution, and a 3-approximation algorithm for the CMSR problem.