RNA secondary structures and their prediction

classification enumeration free energy review graphical representations prediction techniques secondary structure of ribonucleic acids thermodynamic criteria

Mathematics Subject Classification ID

Applications of mathematical programming (90C90) Dynamic programming (90C39) Software, source code, etc. for problems pertaining to biology (92-04) Physiological, cellular and medical topics (92Cxx)

Cites Work

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RNA secondary structure: a complete mathematical analysis
On some new sequences generalizing the Catalan and Motzkin numbers
Algorithms for Loop Matchings
Matching Sequences under Deletion/Insertion Constraints
Shortcuts, diversions, and maximal chains in partially ordered sets
Technical Note—Determining All Optimal and Near-Optimal Solutions when Solving Shortest Path Problems by Dynamic Programming
Sequence alignments in the neighborhood of the optimum with general application to dynamic programming

Cited In (54)

New approximation algorithms for RNA secondary structures prediction problems by local search
A study of primer design with \(w\)-constacyclic shift over \(\mathbb{F}_4\)
Construction of DNA codes with multiple constrained properties
A Sparsified Four-Russian Algorithm for RNA Folding
Exact matching of RNA secondary structure patterns
Transformations of partial matchings
Linear trees and RNA secondary structure
Generic properties of combinatory maps: Neutral networks of RNA secondary structures
Weighted sequence graphs: Boosting iterated dynamic programming using locally suboptimal solutions
Speeding up the dynamic algorithm for planar RNA folding
A new algorithm for generation of different types of RNA
Narayana number, Chebyshev polynomial and Motzkin path on RNA abstract shapes
Average complexity of the Jiang-Wang-Zhang pairwise tree alignment algorithm and of an RNA secondary structure alignment algorithm
Reidys' and Stadler's metrics for RNA contact structures
A continuous analogue for RNA folding
On RNA-RNA interaction structures of fixed topological genus
RNA secondary structures: an approach through pseudoknots and fatgraphs
RNA secondary structure, permutations, and statistics
Sequence comparison with concave weighting functions
Computing similarity between RNA structures
Loop homology of bi-secondary structures
RNA secondary structures in a polymer-zeta model how foldings should be shaped for sparsification to establish a linear speedup
A new algorithm for computing similarity between RNA structures
Fast Fourier transform for fitness landscapes
Some statistics on generalized Motzkin paths with vertical steps
Mathematical and biological modelling of RNA secondary structure and its effects on gene expression
Chance and necessity in evolution: lessons from RNA
RNA structures with pseudo-knots: graph-theoretical, combinatorial, and statistical properties
Asymptotic enumeration of RNA structures with pseudoknots
Modeling RNA secondary structures. I: Mathematical structural model for predicting RNA secondary structures
Neutral networks of sequence to shape maps
Overlapping genes coded in the 3'-to-5'-direction in mitochondrial genes and 3'-to-5' polymerization of non-complementary RNA by an `invertase'
The rainbow spectrum of RNA secondary structures
On edge-colored interior planar graphs on a circle and the expected number of RNA secondary structures
Combinatorics of RNA secondary structures
Modeling RNA secondary structures. II: The geometric structural solution for tRNA
Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots
Asymptotic enumeration of RNA secondary structure
A new family of metrics for biopolymer contact structures
General combinatorics of RNA secondary structure
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Messenger RNA Information: Its Implication in Protein Structure Determination and Others
On the computational complexity of 2-interval pattern matching problems
Rapid dynamic programming algorithms for RNA secondary structure
Loop homology of bi-secondary structures. II
Combinatorics of RNA structures with pseudoknots
Modelling molecular stability in the RNA world
Variations on RNA folding and alignment: Lessons from Benasque
The role of the peptides at the origin of life
Evolving towards the hypercycle: a spatial model of molecular evolution
Central and local limit theorems for RNA structures
RNA folding kinetics using Monte Carlo and Gillespie algorithms
RNA secondary structures with given motif specification: combinatorics and algorithms
A phase transition for the minimum free energy of secondary structures of a random RNA

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