Approximating discrete collections via local improvements
Proceedings of the sixth annual ACM-SIAM symposium on Discrete algorithms
Removing Noise and Ambiguities from Comparative Maps in Rearrangement Analysis
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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
On the parameterized complexity of some optimization problems related to multiple-interval graphs
CPM'10 Proceedings of the 21st annual conference on Combinatorial pattern matching
Efficient exact and approximate algorithms for the complement of maximal strip recovery
AAIM'10 Proceedings of the 6th international conference on Algorithmic aspects in information and management
Inapproximability of maximal strip recovery: II
FAW'10 Proceedings of the 4th international conference on Frontiers in algorithmics
Exact and approximation algorithms for the complementary maximal strip recovery problem
Journal of Combinatorial Optimization
Algorithms for the extraction of synteny blocks from comparative maps
WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
Inapproximability 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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An essential task in comparative genomics is usually to decompose two or more genomes into synteny blocks, that is, segments of chromosomes with similar contents. In this paper, we study the MAXIMAL STRIP RECOVERY problem (MSR) [Zheng et al. 07], which aims at finding an optimal decomposition of a set of genomes into synteny blocks, amidst possible noise and ambiguities. We present a panel of new or improved FPT and approximation algorithms for the MSR problem and its variants. Our main results include the first FPT algorithm for the variant δ-gap-MSR-d, an FPT algorithm for CMSR-d and δ-gap-CMSR-d running in time O(2.360k poly(nd)), where k is the number of markers or genes considered as erroneous, and a (d + 1.5)-approximation algorithm for CMSR-d and δ-gap-CMSR-d.