Trapezoid graphs and their coloring
Discrete Applied Mathematics
New clique and independent set algorithms for circle graphs
Discrete Applied Mathematics
Ordered and Unordered Tree Inclusion
SIAM Journal on Computing
Trapezoid graphs and generalizations, geometry and algorithms
Discrete Applied Mathematics
Computational geometry: algorithms and applications
Computational geometry: algorithms and applications
SODA '02 Proceedings of the thirteenth annual ACM-SIAM symposium on Discrete algorithms
Concrete Math
Computers and Intractability: A Guide to the Theory of NP-Completeness
Computers and Intractability: A Guide to the Theory of NP-Completeness
Pattern Matching Problems over 2-Interval Sets
CPM '02 Proceedings of the 13th Annual Symposium on Combinatorial Pattern Matching
CPM '02 Proceedings of the 13th Annual Symposium on Combinatorial Pattern Matching
Algorithmic Aspects of Protein Structure Similarity
FOCS '99 Proceedings of the 40th Annual Symposium on Foundations of Computer Science
Algorithmic Graph Theory and Perfect Graphs (Annals of Discrete Mathematics, Vol 57)
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A Polynomial-Time Algorithm for the Matching of Crossing Contact-Map Patterns
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Pattern matching for arc-annotated sequences
ACM Transactions on Algorithms (TALG)
Optimization problems in multiple-interval graphs
SODA '07 Proceedings of the eighteenth annual ACM-SIAM symposium on Discrete algorithms
Extracting constrained 2-interval subsets in 2-interval sets
Theoretical Computer Science
Approximating the 2-interval pattern problem
Theoretical Computer Science
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
On two open problems of 2-interval patterns
Theoretical Computer Science
On the Tractability of Maximal Strip Recovery
TAMC '09 Proceedings of the 6th Annual Conference on Theory and Applications of Models of Computation
Bounds arc consistency for weighted CSPs
Journal of Artificial Intelligence Research
Greedy colorings for the binary paintshop problem
Journal of Discrete Algorithms
Complexity issues in color-preserving graph embeddings
Theoretical Computer Science
Fast Arc-Annotated Subsequence Matching in Linear Space
SOFSEM '10 Proceedings of the 36th Conference on Current Trends in Theory and Practice of Computer Science
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
Comparing RNA structures: towards an intermediate model between the edit and the LAPCS problems
BSB'07 Proceedings of the 2nd Brazilian conference on Advances in bioinformatics and computational biology
On restrictions of balanced 2-interval graphs
WG'07 Proceedings of the 33rd international conference on Graph-theoretic concepts in computer science
Finding common structured patterns in linear graphs
Theoretical Computer Science
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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
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
Recognizing d-interval graphs and d-track interval graphs
FAW'10 Proceedings of the 4th international conference on Frontiers in algorithmics
Finding common RNA pseudoknot structures in polynomial time
Journal of Discrete Algorithms
Approximation of RNA multiple structural alignment
Journal of Discrete Algorithms
On the complexity of the crossing contact map pattern matching problem
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Approximation of RNA multiple structural alignment
CPM'06 Proceedings of the 17th Annual conference on Combinatorial Pattern Matching
Finding common RNA pseudoknot structures in polynomial time
CPM'06 Proceedings of the 17th Annual conference on Combinatorial Pattern Matching
Approximating the 2-interval pattern problem
ESA'05 Proceedings of the 13th annual European conference on Algorithms
How to compare arc-annotated sequences: the alignment hierarchy
SPIRE'06 Proceedings of the 13th international conference on String Processing and Information Retrieval
Faster pattern matching algorithm for arc-annotated sequences
Proceedings of the 2005 international conference on Federation over the Web
Improved algorithms for largest cardinality 2-interval pattern problem
ISAAC'05 Proceedings of the 16th international conference on Algorithms and Computation
What makes the arc-preserving subsequence problem hard?
ICCS'05 Proceedings of the 5th international conference on Computational Science - Volume Part II
What makes the arc-preserving subsequence problem hard?
Transactions on Computational Systems Biology II
Parameterized algorithms for inclusion of linear matchings
ISAAC'11 Proceedings of the 22nd international conference on Algorithms and Computation
LATIN'12 Proceedings of the 10th Latin American international conference on Theoretical Informatics
Pattern matching in protein-protein interaction graphs
FCT'07 Proceedings of the 16th international conference on Fundamentals of Computation Theory
Common structured patterns in linear graphs: approximation and combinatorics
CPM'07 Proceedings of the 18th annual conference on Combinatorial Pattern Matching
| Hi-index | 5.23 |
The focus of this paper is on the computational complexity of pattern matching problems over set of 2-intervals. These problems occur in the context of molecular biology when a structured pattern, i.e., a RNA secondary structure given in the form of a 2-interval pattern, has to be found in a sequence database. We show that finding a 2-interval pattern in a set of 2-intervals is a NP-complete problem even if no 2-interval of the pattern precedes the other, but can be solved in polynomial time for several interesting special cases. In particular, it is shown that the pseudo-knot free RNA secondary structure case is polynomial time solvable in our 2-interval formalism. Also, we investigate the computational complexity of finding the longest 2-interval pattern in a set of 2-intervals and prove several NP-completeness results as well as polynomial time solvable special cases.