RNA secondary structures with given motif specification: combinatorics and algorithms

DOI10.1007/s11538-023-01128-5OpenAlexW4320485804MaRDI QIDQ2687721

Ricky X. F. Chen, Christian M. Reidys, Michael S. Waterman

Publication date: 7 March 2023

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

Full work available at URL: https://doi.org/10.1007/s11538-023-01128-5

zbMATH Keywords

loophelixplane treeRNA secondary structureuniform samplingrake decomposition

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Chemical graph theory (05C92)

Uses Software

• RNAfold
• RNAsubopt
• Mfold

Cites Work

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• On trees and noncrossing partitions
• Enumerative aspects of secondary structures
• Noncrossing partitions
• On Finding All Suboptimal Foldings of an RNA Molecule
• A general bijective algorithm for trees.
• Combinatorics of RNA Hairpins and Cloverleaves
• Boltzmann Samplers for the Random Generation of Combinatorial Structures