Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots

DOI10.1016/S0166-218X(00)00186-4zbMATH Open0956.92019MaRDI QIDQ1585319FDOQ1585319

Publication date: 17 March 2001

Published in: Discrete Applied Mathematics (Search for Journal in Brave)

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approximation algorithm RNA secondary structure pseudoknot

Complexity and performance of numerical algorithms (65Y20) Applications of mathematical programming (90C90) Biochemistry, molecular biology (92C40) Dynamic programming (90C39) Computational methods for problems pertaining to biology (92-08)

Cites Work

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The Complexity of Some Problems on Subsequences and Supersequences
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RNA secondary structure: a complete mathematical analysis
TAL recognition in \(O(M(n^2))\) time
Planar graphs: Theory and algorithms
Approximation and exact algorithms for RNA secondary structure prediction and recognition of stochastic context-free languages
RNA secondary structures and their prediction
Dynamic programming with convexity, concavity and sparsity

Cited In (44)

Title not available (Why is that?)
Structural Alignment of Pseudoknotted RNA
Improved approximation algorithm for the maximum base pair stackings problem in RNA secondary structures prediction
Predicting RNA secondary structures with pseudoknots by MCMC sampling
New approximation algorithms for RNA secondary structures prediction problems by local search
Rapid ab initio prediction of RNA pseudoknots via graph tree decomposition
Title not available (Why is that?)
A new method for prediction of RNA secondary structure with pseudoknots, based on helix removal and refinement
RNA secondary structure prediction algorithm based on fast dynamic weighted matching
Automated design of dynamic programming schemes for RNA folding with pseudoknots
A genetic algorithm for predicting RNA pseudoknot structures
New models and algorithms for RNA pseudoknot order assignment
Algebraic dynamic programming for multiple context-free grammars
Computational prediction of nucleic acid secondary structure: Methods, applications, and challenges
Posets and spaces of \(k\)-noncrossing RNA structures
Tree adjoining grammars for RNA structure prediction
Classifying RNA pseudoknotted structures
Prediction for RNA planar pseudoknots
Moduli spaces and macromolecules
An RNA folding algorithm including pseudoknots based on dynamic weighted matching
Approximating the 2-interval pattern problem
Local connectivity of neutral networks
Title not available (Why is that?)
Asymptotic enumeration of RNA structures with pseudoknots
Improved Approximation Algorithms for Predicting RNA Secondary Structures with Arbitrary Pseudoknots
Stacks in canonical RNA pseudoknot structures
Impact of the energy model on the complexity of RNA folding with pseudoknots
Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots
Title not available (Why is that?)
Fixed-parameter algorithms for protein similarity search under mRNA structure constraints
An RNA folding algorithm based on dynamic weighted matching
Automata, Languages and Programming
Pseudoknot-generating operation
Pseudoknot-generating operation
Computational Science – ICCS 2005
On the page number of RNA secondary structures with pseudoknots
Finding common RNA pseudoknot structures in polynomial time
Combinatorial design of pseudoknot RNA
Computing and Combinatorics
Combinatorics of RNA structures with pseudoknots
Counting RNA pseudoknotted structures (extended abstract)
Speedup of RNA pseudoknotted secondary structure recurrence computation with the four-Russians method
Polynomial algorithms for protein similarity search for restricted mRNA structures
Fatgraph models of RNA structure

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