On the page number of RNA secondary structures with pseudoknots

DOI10.1007/s00285-011-0493-6zbMath1252.92021OpenAlexW2066299005WikidataQ51476527 ScholiaQ51476527MaRDI QIDQ694703

Evangelos Kranakis, Jorge Urrutia, Peter Clote, Ivan Dotu, Danny Krizanc, Stefan Dobrev

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

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

Related Items

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

Uses Software

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

Cites Work

• RNA structures with pseudo-knots: graph-theoretical, combinatorial, and statistical properties
• Rapid ab initio prediction of RNA pseudoknots via graph tree decomposition
• Predicting RNA secondary structures with pseudoknots by MCMC sampling
• PSSMTS: Position specific scoring matrices on tree structures
• On the decomposition of \(k\)-noncrossing RNA structures
• The square of a chordal graph
• Covering and coloring polygon-circle graphs
• Algorithmic graph theory and perfect graphs
• The graph genus problem is NP-complete
• Random k -noncrossing RNA structures
• The Complexity of Coloring Circular Arcs and Chords
• Embedding Graphs in Books: A Layout Problem with Applications to VLSI Design
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