How to Compare Arc-Annotated Sequences: The Alignment Hierarchy

DOI10.1007/11880561_24MaRDI QIDQ3523001zbMATH OpenOpenAlexFDO

Authors Guillaume Blin, H. Touzet

Publication date 4 September 2008

Published in String Processing and Information Retrieval (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/11880561_24

zbMATH Keywords

algorithmarc-annotated sequencescomputational biologyedit distanceNP-hardnessRNA structures

Mathematics Subject Classification ID

Complexity and performance of numerical algorithms (65Y20) Computational difficulty of problems (lower bounds, completeness, difficulty of approximation, etc.) (68Q17) Algorithms on strings (68W32) Biochemistry, molecular biology (92C40) Systems biology, networks (92C42)

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Cited in

(5)

• Fast arc-annotated subsequence matching in linear space
• Forest Alignment with Affine Gaps and Anchors
• Forest alignment with affine gaps and anchors, applied in RNA structure comparison
• A new algorithm for aligning nested arc-annotated sequences under arbitrary weight schemes
• Average complexity of the Jiang-Wang-Zhang pairwise tree alignment algorithm and of an RNA secondary structure alignment algorithm

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