On the page number of RNA secondary structures with pseudoknots

DOI10.1007/S00285-011-0493-6MaRDI QIDQ694703zbMATH OpenOpenAlexWikidataFDO

Authors Peter Clote, Stefan Dobrev, Ivan Dotu, Evangelos Kranakis, D. Krizanc, J. Urrutia

Publication date 13 December 2012

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

Full work available at URL https://doi.org/10.1007/s00285-011-0493-6

Mathematics Subject Classification ID

Complexity and performance of numerical algorithms (65Y20) Applications of mathematical programming (90C90) Biochemistry, molecular biology (92C40) Graph algorithms (graph-theoretic aspects) (05C85) Analysis of algorithms and problem complexity (68Q25) Approximation algorithms (68W25)

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Cites work

• scientific article; zbMATH DE number 4162324 (Why is no real title available?)
• scientific article; zbMATH DE number 3706474 (Why is no real title available?)
• scientific article; zbMATH DE number 821271 (Why is no real title available?)
• Algorithmic graph theory and perfect graphs
• Covering and coloring polygon-circle graphs
• Embedding Graphs in Books: A Layout Problem with Applications to VLSI Design
• Large-\(N\) random matrices for RNA folding
• On the decomposition of \(k\)-noncrossing RNA structures
• PSSMTS: Position specific scoring matrices on tree structures
• Predicting RNA secondary structures with pseudoknots by MCMC sampling
• RNA structures with pseudo-knots: graph-theoretical, combinatorial, and statistical properties
• Random \(k\)-noncrossing RNA structures
• Rapid ab initio prediction of RNA pseudoknots via graph tree decomposition
• The Complexity of Coloring Circular Arcs and Chords
• The graph genus problem is NP-complete
• The square of a chordal graph

Cited in

(10)

• Visualization of RNA secondary structure with pseudoknots
• Combinatorics of locally optimal RNA secondary structures
• Psybrackets, pseudoknots and singular knots
• The Local Queue Number of Graphs with Bounded Treewidth
• Psyquandle coloring quivers
• Fixed-parameter tractability for book drawing with bounded number of crossings per edge
• Asymptotic number of hairpins of saturated RNA secondary structures
• Cocycle enhancements of psyquandle counting invariants
• Crossings and nestings for arc-coloured permutations and automation
• A graphical criterion of planarity for RNA secondary structures with pseudoknots in Rivas-Eddy class

Describes a project that uses

Uses Software

• Pfold
• ProbKnot
• HotKnots
• jViz.Rna
• IPknot
• Mfold
• UNAFold
• tRNAscan-SE

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