Rapid dynamic programming algorithms for RNA secondary structure
Advances in Applied Mathematics
Tree graphs of RNA secondary structures and their comparisons
Computers and Biomedical Research
Classifier systems and genetic algorithms
Artificial Intelligence
Fuzzy logic, neural networks, and soft computing
Communications of the ACM
A massively parallel genetic algorithm for RNA secondary structure prediction
The Journal of Supercomputing
The nature of statistical learning theory
The nature of statistical learning theory
Fuzzy dynamic programming: main developments and applications
Fuzzy Sets and Systems - Special issue on fuzzy optimization
Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots
Discrete Applied Mathematics - Special volume on combinatorial molecular biology
Neural Networks: A Comprehensive Foundation
Neural Networks: A Comprehensive Foundation
Genetic Algorithms in Search, Optimization and Machine Learning
Genetic Algorithms in Search, Optimization and Machine Learning
Guest editorial: soft computing data mining
Information Sciences: an International Journal - Special issue: Soft computing data mining
A Hopfield Neural Network Based Algorithm for RNA Secondary Structure Prediction
IMSCCS '06 Proceedings of the First International Multi-Symposiums on Computer and Computational Sciences - Volume 1 (IMSCCS'06) - Volume 01
RnaPredict—An Evolutionary Algorithm for RNA Secondary Structure Prediction
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Predicting RNA secondary structure based on the class information and Hopfield network
Computers in Biology and Medicine
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A fuzzy dynamic programming approach to predict RNA secondary structure
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Neural networks for classification: a survey
IEEE Transactions on Systems, Man, and Cybernetics, Part C: Applications and Reviews
Evolutionary computation in bioinformatics: a review
IEEE Transactions on Systems, Man, and Cybernetics, Part C: Applications and Reviews
Fuzzy rough granular self-organizing map and fuzzy rough entropy
Theoretical Computer Science
A Weighted Threshold for Detection of Cancerous miRNA Expressions
Fundamenta Informaticae - To Andrzej Skowron on His 70th Birthday
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Prediction of RNA structure is invaluable in creating new drugs and understanding genetic diseases. Several deterministic algorithms and soft computing-based techniques have been developed for more than a decade to determine the structure from a known RNA sequence. Soft computing gained importance with the need to get approximate solutions for RNA sequences by considering the issues related with kinetic effects, cotranscriptional folding, and estimation of certain energy parameters. A brief description of some of the soft computing-based techniques, developed for RNA secondary structure prediction, is presented along with their relevance. The basic concepts of RNA and its different structural elements like helix, bulge, hairpin loop, internal loop, and multiloop are described. These are followed by different methodologies, employing genetic algorithms, artificial neural networks, and fuzzy logic. The role of various metaheuristics, like simulated annealing, particle swarm optimization, ant colony optimization, and tabu search is also discussed. A relative comparison among different techniques, in predicting 12 known RNA secondary structures, is presented, as an example. Future challenging issues are then mentioned.