The parameterized complexity of sequence alignment and consensus
Theoretical Computer Science
Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
New methods for 3-SAT decision and worst-case analysis
Theoretical Computer Science
Near optimal multiple alignment within a band in polynomial time
STOC '00 Proceedings of the thirty-second annual ACM symposium on Theory of computing
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
Faster exact algorithms for hard problems: a parameterized point of view
Discrete Mathematics
Experimenting an approximation algorithm for the LCS
Discrete Applied Mathematics
MFCS '94 Proceedings of the 19th International Symposium on Mathematical Foundations of Computer Science 1994
The Longest Common Subsequence Problem for Sequences with Nested Arc Annotations
ICALP '01 Proceedings of the 28th International Colloquium on Automata, Languages and Programming,
Finding Common Subsequences with Arcs and Pseudoknots
CPM '99 Proceedings of the 10th Annual Symposium on Combinatorial Pattern Matching
The Longest Common Subsequence Problem for Arc-Annotated Sequences
COM '00 Proceedings of the 11th 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
Algorithms and complexity for annotated sequence analysis
Algorithms and complexity for annotated sequence analysis
Parameterized Complexity: The Main Ideas and Some Research Frontiers
ISAAC '01 Proceedings of the 12th International Symposium on Algorithms and Computation
Parameterized Complexity
Pattern Matching for Arc-Annotated Sequences
FST TCS '02 Proceedings of the 22nd Conference Kanpur on Foundations of Software Technology and Theoretical Computer Science
On the computational complexity of 2-interval pattern matching problems
Theoretical Computer Science
Extracting constrained 2-interval subsets in 2-interval sets
Theoretical Computer Science
Finding occurrences of protein complexes in protein-protein interaction graphs
Journal of Discrete Algorithms
Finding exact and maximum occurrences of protein complexes in protein-protein interaction graphs
MFCS'05 Proceedings of the 30th international conference on Mathematical Foundations of Computer Science
What makes the arc-preserving subsequence problem hard?
Transactions on Computational Systems Biology II
Normalized similarity of RNA sequences
SPIRE'05 Proceedings of the 12th international conference on String Processing and Information Retrieval
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We present exact algorithms for the NP-complete Longest Common Subsequence problem for sequences with nested arc annotations, a problem occurring in structure comparison of RNA. Given two sequences of length at most n and nested arc structure, our algorithm determines (if existent) in time O(3.31k1+k2驴n) an arc-preserving subsequence of both sequences, which can be obtained by deleting (together with corresponding arcs) k1 letters from the first and k2 letters from the second sequence. Thus, the problem is fixed-parameter tractable when parameterized by the number of deletions. This complements known approximation results which give a quadratic time factor-2-approximation for the general and polynomial time approximation schemes for restricted versions of the problem. In addition, we obtain further fixed-parameter tractability results for these restricted versions.