Forest Alignment with Affine Gaps and Anchors

DOI10.1007/978-3-642-21458-5_11zbMath1339.68212OpenAlexW139823962MaRDI QIDQ3011847

Robert Giegerich, Stefanie Schirmer

Publication date: 29 June 2011

Published in: Combinatorial Pattern Matching (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1007/978-3-642-21458-5_11

zbMATH Keywords

affine gap costsanchored alignmentforest alignmentRNA structure alignment

Mathematics Subject Classification ID

Analysis of algorithms and problem complexity (68Q25) Graph theory (including graph drawing) in computer science (68R10) Protein sequences, DNA sequences (92D20)

Related Items (3)

Algebraic dynamic programming on trees ⋮ Large-scale frequent stem pattern mining in RNA families ⋮ Modeling dynamic programming problems over sequences and trees with inverse coupled rewrite systems

Uses Software

• RNAforester

Cites Work

• Alignment of trees -- an alternative to tree edit
• Tree edit distance with gaps
• An algebraic view of the relation between largest common subtrees and smallest common supertrees
• Simple Fast Algorithms for the Editing Distance between Trees and Related Problems
• Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots
• How to Compare Arc-Annotated Sequences: The Alignment Hierarchy
• Fast RNA Structure Alignment for Crossing Input Structures
• The Tree-to-Tree Correction Problem
• Combinatorial Pattern Matching

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