Fast RNA Structure Alignment for Crossing Input Structures

DOI10.1007/978-3-642-02441-2_21MaRDI QIDQ3637116zbMATH OpenOpenAlexFDO

Authors Rolf Backofen, Gad M. Landau, Mathias Möhl, Dekel Tsur, Oren Weimann

Publication date 7 July 2009

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

Full work available at URL https://doi.org/10.1007/978-3-642-02441-2_21

zbMATH Keywords

RNAsequence structure alignmentsimultaneous alignment and folding

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Analysis of algorithms and problem complexity (68Q25) Algorithms on strings (68W32)

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Cites work

• scientific article; zbMATH DE number 1305084 (Why is no real title available?)
• A Study of Accessible Motifs and RNA Folding Complexity
• An Optimal Decomposition Algorithm for Tree Edit Distance
• Approximation and exact algorithms for RNA secondary structure prediction and recognition of stochastic context-free languages
• Finding Common RNA Pseudoknot Structures in Polynomial Time
• RNA secondary structure: a complete mathematical analysis
• Simultaneous Solution of the RNA Folding, Alignment and Protosequence Problems

Cited in

(6)

• Forest alignment with affine gaps and anchors, applied in RNA structure comparison
• Fast RNA structure alignment for crossing input structures
• Fast and accurate structure probability estimation for simultaneous alignment and folding of RNAs
• Forest Alignment with Affine Gaps and Anchors
• Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots
• Fast arc-annotated subsequence matching in linear space

Describes a project that uses

Uses Software

• CONTRAfold

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