Introduction to Formal Language Theory
Introduction to Formal Language Theory
Alignment Of Protein Structures With A Memetic Evolutionary Algorithm
GECCO '02 Proceedings of the Genetic and Evolutionary Computation Conference
Pattern Matching for Arc-Annotated Sequences
FST TCS '02 Proceedings of the 22nd Conference Kanpur on Foundations of Software Technology and Theoretical Computer Science
Algorithmic Aspects of Protein Structure Similarity
FOCS '99 Proceedings of the 40th Annual Symposium on Foundations of Computer Science
Kernel Methods for Pattern Analysis
Kernel Methods for Pattern Analysis
On the computational complexity of 2-interval pattern matching problems
Theoretical Computer Science
Computing the similarity of two sequences with nested arc annotations
Theoretical Computer Science
Parameterized Complexity
Pattern matching for arc-annotated sequences
ACM Transactions on Algorithms (TALG)
On two open problems of 2-interval patterns
Theoretical Computer Science
Finding common structured patterns in linear graphs
Theoretical Computer Science
Finding common RNA pseudoknot structures in polynomial time
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
Finding common RNA pseudoknot structures in polynomial time
CPM'06 Proceedings of the 17th Annual conference on Combinatorial Pattern Matching
Protein surface characterization using an invariant descriptor
Journal of Biomedical Imaging - Special issue on Mathematical Methods for Images and Surfaces 2011
Common structured patterns in linear graphs: approximation and combinatorics
CPM'07 Proceedings of the 18th annual conference on Combinatorial Pattern Matching
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Contact maps are a model to capture the core information in the structure of biological molecules, e.g., proteins. A contact map consists of an ordered set S of elements (representing a protein's sequence of amino acids), and a set A of element pairs of S, called arcs (representing amino acids which are closely neighbored in the structure). Given two contact maps (S,A) and (S_p,A_p) with |A|\geq |A_p|, the Contact Map Pattern Matching (CMPM) problem asks whether the "pattern驴(S_p,A_p) "occurs驴 in (S,A), i.e., informally stated, whether there is a subset of |A_p| arcs in A whose arc structure coincides with A_p. CMPM captures the biological question of finding structural motifs in protein structures. In general, CMPM is NP-hard. In this paper, we show that CMPM is solvable in O(|A|^6|A_p|^2) time when the pattern is \{