Classifying RNA pseudoknotted structures

DOI10.1016/J.TCS.2004.03.042zbMATH Open1043.92008OpenAlexW2013195357MaRDI QIDQ596125FDOQ596125

Authors Anne Condon, Beth Davy, Baharak Rastegari, Shelly Zhao, Finbarr Tarrant 

Publication date 10 August 2004

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

Full work available at URL https://eprints.soton.ac.uk/426392/1/1_s2.0_S0304397504001938_main.pdf

zbMATH Keywords

RNA secondary structureClassification of structuresPseudoknots

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Computational methods for problems pertaining to biology (92-08) Biophysics (92C05)

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Cites work

• Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots
• Tree adjoining grammars for RNA structure prediction

Cited in

(15)

• Predicting RNA secondary structures with pseudoknots by MCMC sampling
• A new method for prediction of RNA secondary structure with pseudoknots, based on helix removal and refinement
• Algebraic dynamic programming for multiple context-free grammars
• Posets and spaces of \(k\)-noncrossing RNA structures
• An RNA secondary structure prediction method based on minimum and suboptimal free energy structures
• A grammatical approach to RNA-RNA interaction prediction
• Prediction for RNA planar pseudoknots
• Properties of RNA secondary structure matching models
• Comparing two \(K\)-category assignments by a \(K\)-category correlation coefficient
• Automata, Languages and Programming
• Pseudoknot-generating operation
• A graphical criterion of planarity for RNA secondary structures with pseudoknots in Rivas-Eddy class
• Combinatorial design of pseudoknot RNA
• Counting RNA pseudoknotted structures (extended abstract)
• Fatgraph models of RNA structure

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