Some APX-completeness results for cubic graphs
Theoretical Computer Science
Non-approximability results for optimization problems on bounded degree instances
STOC '01 Proceedings of the thirty-third annual ACM symposium on Theory of computing
SIAM Journal on Computing
Complexity of approximating bounded variants of optimization problems
Theoretical Computer Science - Foundations of computation theory (FCT 2003)
On the complexity of approximating k-set packing
Computational Complexity
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
Approximation Algorithms for Predicting RNA Secondary Structures with Arbitrary Pseudoknots
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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
On the parameterized complexity of some optimization problems related to multiple-interval graphs
Theoretical Computer Science
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
Theoretical Computer Science
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
Exact and approximation algorithms for the complementary maximal strip recovery problem
Journal of Combinatorial Optimization
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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Maximal Strip Recovery (MSR) is an optimization problem proposed by Zheng, Zhu, and Sankoff for reliably recovering syntenic blocks from genomic maps in the midst of noise and ambiguities. Given d genomic maps as sequences of gene markers, the objective of MSR-d is to find d subsequences, one subsequence of each genomic map, such that the total length of syntenic blocks in these subsequences is maximized. In our recent paper entitled "Inapproximability of Maximal Strip Recovery" in ISAAC 2009, we proved that MSR-d is APX-hard for any constant d ≥ 2, and presented the first explicit lower bounds for approximating MSR-2, MSR-3, and MSR-4, even for the most basic version of the problem in which all markers are distinct and appear in positive orientation in each genomic map. In this paper, we present several further inapproximability results for MSR-d and its variants CMSR-d, δ-gap-MSR-d, and δ-gap-CMSR-d. One of our main results is that MSR-d is NP-hard to approximate within Ω(d/log d) even if all markers appear in positive orientation in each genomic map. From the other direction, we show that there is a polynomial-time 2d-approximation algorithm for MSR-d even if d is not a constant but is part of the input.