DARN! A weighted constraint solver for RNA motif localization

DOI10.1007/S10601-007-9033-9MaRDI QIDQ941671zbMATH OpenOpenAlexFDO

Authors Matthias Zytnicki, Christine Gaspin, Thomas Schiex

Publication date 2 September 2008

Published in Constraints (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/s10601-007-9033-9

zbMATH Keywords

ncRNA

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Nonnumerical algorithms (68W05) Computational methods for problems pertaining to biology (92-08) Cell biology (92C37)

Recommendations

• Local exact pattern matching for non-fixed RNA structures
• Exact matching of RNA secondary structure patterns
• RNA secondary structure determination and representation based on constraints satisfaction
• String Processing and Information Retrieval
• Structural Alignment of Pseudoknotted RNA

Cites work

• scientific article; zbMATH DE number 1754502 (Why is no real title available?)
• On the computational complexity of 2-interval pattern matching problems
• Replacing suffix trees with enhanced suffix arrays
• Solving weighted CSP by maintaining arc consistency

Cited in

(7)

• Seed-Based Exclusion Method for Non-coding RNA Gene Search
• Tractability in constraint satisfaction problems: a survey
• The Nemhauser-Trotter reduction and lifted message passing for the weighted CSP
• SWORD: Genetic algorithm tool for protein-RNA interaction motifs recognition
• Valued constraint satisfaction problems
• DARN!
• Shared subspace-based radial basis function neural network for identifying ncRNAs subcellular localization

Describes a project that uses

Uses Software

• Rnamotif
• Rfam
• Rnabob
• Palingol

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