Trapezoid graphs and their coloring
Discrete Applied Mathematics
Trapezoid graphs and generalizations, geometry and algorithms
Discrete Applied Mathematics
Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots
Discrete Applied Mathematics - Special volume on combinatorial molecular biology
SODA '02 Proceedings of the thirteenth annual ACM-SIAM symposium on Discrete algorithms
BIBE '01 Proceedings of the 2nd IEEE International Symposium on Bioinformatics and Bioengineering
On the computational complexity of 2-interval pattern matching problems
Theoretical Computer Science
Optimization problems in multiple-interval graphs
SODA '07 Proceedings of the eighteenth annual ACM-SIAM symposium on Discrete algorithms
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
On Recovering Syntenic Blocks from Comparative Maps
COCOA 2008 Proceedings of the 2nd international conference on Combinatorial Optimization and Applications
On the parameterized complexity of multiple-interval graph problems
Theoretical Computer Science
The 2-Interval Pattern Matching Problems and Its Application to ncRNA Scanning
BICoB '09 Proceedings of the 1st International Conference on Bioinformatics and Computational Biology
Optimization problems in multiple-interval graphs
ACM Transactions on Algorithms (TALG)
Delta: a toolset for the structural analysis of biological sequences on a 3D triangular lattice
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
On restrictions of balanced 2-interval graphs
WG'07 Proceedings of the 33rd international conference on Graph-theoretic concepts in computer science
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
On the approximability of comparing genomes with duplicates
WALCOM'08 Proceedings of the 2nd international conference on Algorithms and computation
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
On the complexity of the crossing contact map pattern matching problem
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
How to compare arc-annotated sequences: the alignment hierarchy
SPIRE'06 Proceedings of the 13th international conference on String Processing and Information Retrieval
Improved algorithms for largest cardinality 2-interval pattern problem
ISAAC'05 Proceedings of the 16th international conference on Algorithms and Computation
Common structured patterns in linear graphs: approximation and combinatorics
CPM'07 Proceedings of the 18th annual conference on Combinatorial Pattern Matching
The maximum clique problem in multiple interval graphs (extended abstract)
WG'12 Proceedings of the 38th international conference on Graph-Theoretic Concepts in Computer Science
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We address the problem of approximating the 2-Interval Pattern problem over its various models and restrictions. This problem, which is motivated by RNA secondary structure prediction, asks to find a maximum cardinality subset of a 2-interval set with respect to some prespecified model. For each such model, we give varying approximation quality depending on the different possible restrictions imposed on the input 2-interval set.