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
On Some Tighter Inapproximability Results (Extended Abstract)
ICAL '99 Proceedings of the 26th International Colloquium on Automata, Languages and Programming
Hardness of approximation for non-overlapping local alignments
Discrete Applied Mathematics
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 unsigned translocation distance
Theoretical Computer Science
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
Non-approximability of weighted multiple sequence alignment for arbitrary metrics
Information Processing Letters
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
Theoretical Computer Science
Paired approximation problems and incompatible inapproximabilities
SODA '10 Proceedings of the twenty-first annual ACM-SIAM symposium on Discrete Algorithms
Inapproximability of maximal strip recovery: II
FAW'10 Proceedings of the 4th international conference on Frontiers in algorithmics
Tractability and approximability of maximal strip recovery
CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
Algorithms for the extraction of synteny blocks from comparative maps
WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
Tractability and approximability of maximal strip recovery
Theoretical Computer Science
Maximal strip recovery problem with gaps: Hardness and approximation algorithms
Journal of Discrete Algorithms
Hi-index | 5.23 |
In comparative genomics, the first step of sequence analysis is usually to decompose two or more genomes into syntenic blocks that are segments of homologous chromosomes. For the reliable recovery of syntenic blocks, noise and ambiguities in the genomic maps need to be removed first. 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. For any constant d=2, a polynomial-time 2d-approximation for MSR-d was previously known. In this paper, we show that for any d=2, MSR-d is APX-hard, even for the most basic version of the problem in which all gene markers are distinct and appear in positive orientation in each genomic map. Moreover, we provide the first explicit lower bounds on approximating MSR-d for all d=2. In particular, we show that MSR-d is NP-hard to approximate within @W(d/logd). From the other direction, we show that the previous 2d-approximation for MSR-d can be optimized into a polynomial-time algorithm even if d is not a constant but is part of the input. We then extend our inapproximability results to several related problems including CMSR-d, @d-gap-MSR-d, and @d-gap-CMSR-d.