Pattern matching for arc-annotated sequences

DOI10.1145/1125994.1125997MaRDI QIDQ2944505zbMATH OpenOpenAlexFDO

Authors Jens Gramm, Jiong Guo, Rolf Niedermeier

Publication date 2 September 2015

Published in ACM Transactions on Algorithms (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1145/1125994.1125997

zbMATH Keywords

dynamic programmingpattern matchingRNA secondary structurearc-annotated sequences

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Dynamic programming (90C39) Computational difficulty of problems (lower bounds, completeness, difficulty of approximation, etc.) (68Q17) Algorithms on strings (68W32)

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(9)

• A faster and more space-efficient algorithm for inferring arc-annotations of RNA sequences through alignment
• Finding occurrences of protein complexes in protein-protein interaction graphs
• Solving longest common subsequence problems via a transformation to the maximum clique problem
• Parameterized complexity of the arc-preserving subsequence problem
• Fast arc-annotated subsequence matching in linear space
• How to Compare Arc-Annotated Sequences: The Alignment Hierarchy
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• Efficient pattern matching for RNA secondary structures
• Fast arc-annotated subsequence matching in linear space

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