Rapid ab initio prediction of RNA pseudoknots via graph tree decomposition

DOI10.1007/s00285-007-0124-4zbMath1143.92016OpenAlexW1986193692WikidataQ51625280 ScholiaQ51625280MaRDI QIDQ938119

Russell L. Malmberg, Jizhen Zhao, Li-Ming Cai

Publication date: 18 August 2008

Published in: Journal of Mathematical Biology (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1007/s00285-007-0124-4

zbMATH Keywords

tree decompositionthermodynamic energytree widthmaximum independent setRNA secondary structure predictionpseudoknot

Mathematics Subject Classification ID

Applications of graph theory (05C90) Applications of mathematical programming (90C90) Biochemistry, molecular biology (92C40) Computational methods for problems pertaining to biology (92-08)

Related Items (2)

Finding Good Decompositions for Dynamic Programming on Dense Graphs ⋮ On the page number of RNA secondary structures with pseudoknots

Uses Software

• RNAshapes
• HotKnots
• Pfold

Cites Work

• Tree adjoining grammars for RNA structure prediction
• Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots
• Graph minors. II. Algorithmic aspects of tree-width
• Algorithms for Loop Matchings
• Biological Sequence Analysis

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