Sparse RNA Folding: Time and Space Efficient Algorithms

DOI10.1007/978-3-642-02441-2_22MaRDI QIDQ3637117zbMATH OpenOpenAlexFDO

Authors Rolf Backofen, Dekel Tsur, Shay Zakov, Michal Ziv-Ukelson

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_22

Mathematics Subject Classification ID

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

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Cites work

• A faster and more space-efficient algorithm for inferring arc-annotations of RNA sequences through alignment
• A linear space algorithm for computing maximal common subsequences
• A Study of Accessible Motifs and RNA Folding Complexity
• Algorithms for the Longest Common Subsequence Problem
• Approximation and exact algorithms for RNA secondary structure prediction and recognition of stochastic context-free languages
• Biological Sequence Analysis
• scientific article; zbMATH DE number 4116366 (Why is no real title available?)
• More algorithms for all-pairs shortest paths in weighted graphs
• RNA secondary structure: a complete mathematical analysis
• Simultaneous Solution of the RNA Folding, Alignment and Protosequence Problems

Cited in

(9)

• Hardness of RNA folding problem with four symbols
• RNA secondary structures in a polymer-zeta model how foldings should be shaped for sparsification to establish a linear speedup
• Fast and accurate structure probability estimation for simultaneous alignment and folding of RNAs
• Sparse RNA folding revisited: space-efficient minimum free energy prediction
• A sparsified Four-Russian algorithm for RNA folding
• Sparse RNA folding: time and space efficient algorithms
• Hardness of RNA folding problem with four symbols
• SparseRNAFoID: sparse RNA pseudoknot-free folding including dangles
• Speeding up the dynamic algorithm for planar RNA folding

Describes a project that uses

Uses Software

• Mfold

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