Forest alignment with affine gaps and anchors, applied in RNA structure comparison

DOI10.1016/J.TCS.2012.07.040MaRDI QIDQ390877zbMATH OpenOpenAlexFDO

Authors Stefanie Schirmer, Robert Giegerich

Publication date 9 January 2014

Published in Theoretical Computer Science (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.tcs.2012.07.040

zbMATH Keywords

affine gap costsanchored alignmentforest alignmentRNA structure alignment

Mathematics Subject Classification ID

Formal languages and automata (68Q45) Protein sequences, DNA sequences (92D20) Graph theory (including graph drawing) in computer science (68R10) Grammars and rewriting systems (68Q42) Algorithms on strings (68W32)

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Cites work

• A discipline of dynamic programming over sequence data
• A global parser for context-free phrase structure grammars
• Alignment of trees -- an alternative to tree edit
• An algebraic view of the relation between largest common subtrees and smallest common supertrees
• Combinatorial Pattern Matching
• Fast RNA Structure Alignment for Crossing Input Structures
• Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots
• How to Compare Arc-Annotated Sequences: The Alignment Hierarchy
• Multiple genome alignment: chaining algorithms revisited
• Recognition and parsing of context-free languages in time n3
• Simple Fast Algorithms for the Editing Distance between Trees and Related Problems
• Simultaneous Solution of the RNA Folding, Alignment and Protosequence Problems
• Tree edit distance with gaps

Cited in

(4)

• Counting, Generating and Sampling Tree Alignments
• Forest Alignment with Affine Gaps and Anchors
• Counting, Generating, Analyzing and Sampling Tree Alignments
• Algorithms and Computation

Describes a project that uses

Uses Software

• RNAforester
• MUMMER

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