Properties of RNA secondary structure matching models

DOI10.2140/INVOLVE.2019.12.257zbMATH Open1403.92198OpenAlexW2897034997WikidataQ60692723 ScholiaQ60692723MaRDI QIDQ1624873FDOQ1624873

Authors Nicole Anderson, Michael Breunig, Kyle Goryl, Manda Riehl, McKenzie Scanlan, Hannah M. Lewis

Publication date 16 November 2018

Published in Involve (Search for Journal in Brave)

Full work available at URL https://doi.org/10.2140/involve.2019.12.257

zbMATH Keywords

perfect matchingscrossing numberRNA secondary structurepseudoknotnesting number

Mathematics Subject Classification ID

Applications of graph theory (05C90) Protein sequences, DNA sequences (92D20)

Recommendations

• Enumerating RNA structures, including pseudoknots of any topology
• Non-crossing matchings
• RNA pseudoknot structures with arc-length \(\geq 3\) and stack-length \(\geq \sigma \)
• Combinatorial design of pseudoknot RNA
• RNA structures with pseudo-knots: graph-theoretical, combinatorial, and statistical properties

Cites work

• A bijection between the set of nesting-similarity classes and L \& P matchings
• Classifying RNA pseudoknotted structures
• Crossings and nestings of matchings and partitions
• The On-Line Encyclopedia of Integer Sequences

Cited in

(7)

• Barrier heights between ground states in a model of RNA secondary structure
• Mathematical and biological modelling of RNA secondary structure and its effects on gene expression
• Exact matching of RNA secondary structure patterns
• Topological transition in disordered planar matching: combinatorial arcs expansion
• Non-crossing matchings
• A bijection between the set of nesting-similarity classes and L \& P matchings
• Modelling molecular stability in the RNA world

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Uses Software

• OEIS

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