• Publications
  • Influence
RnaPredict—An Evolutionary Algorithm for RNA Secondary Structure Prediction
TLDR
RnaPredict is shown to outperform the minimum free energy structures produced by mfold and has comparable performance when compared to sub-optimal structures producedBy mfold. Expand
A permutation-based genetic algorithm for the RNA folding problem: a critical look at selection strategies, crossover operators, and representation issues.
TLDR
The proposed GA predicts which specific canonical base pairs will form hydrogen bonds and build helices, also known as stems, and shows that the Keep-Best Reproduction operator has similar benefits as in the traveling salesman problem domain. Expand
Comparison of P-RnaPredict and mfold - algorithms for RNA secondary structure prediction
TLDR
P-RnaP Predict, a parallel evolutionary algorithm for RNA secondary structure prediction, is presented and is able to predict structures with higher true positive base pair counts and lower false positives than mfold on certain sequences. Expand
SARNA-Predict: Accuracy Improvement of RNA Secondary Structure Prediction Using Permutation-Based Simulated Annealing
TLDR
The usefulness of SARNA-Predict, an RNA secondary structure prediction algorithm based on Simulated Annealing (SA), is demonstrated and there is substantial improvement of prediction accuracy by incorporating a more sophisticated thermodynamic model (efn2). Expand
jViz.Rna -a java tool for RNA secondary structure visualization
TLDR
JViz.Rna is a multiplatform visualization tool capable of displaying RNA secondary structures encoded in a variety of file formats and can easily be further manipulated by the user. Expand
SARNA-Predict: A Study of RNA Secondary Structure Prediction Using Different Annealing Schedules
TLDR
An algorithm for RNA secondary structure prediction based on simulated annealing (SA) that heuristically searches for the structure with a free energy value close to the minimum free energy DeltaG for that strand, within given constraints is presented. Expand
jViz.Rna - An Interactive Graphical Tool for Visualizing RNA Secondary Structure Including Pseudoknots
  • K. Wiese, E. Glen
  • Computer Science
  • 19th IEEE Symposium on Computer-Based Medical…
  • 22 June 2006
TLDR
JViz.Rna is a multi-platform visualization tool capable of displaying RNA secondary structures encoded in a variety of file formats and the unique usage of a spring model for classical structure drawing allows for clear visualization of pseudoknots with minimal overlaps. Expand
The significance of thermodynamic models in the accuracy improvement of RNA secondary structure prediction using permutation-based simulated annealing
TLDR
Significant improvements made to SARNA-Predict, an RNA secondary structure prediction algorithm based on Simulated Annealing (SA), are discussed, which shows results which surpass the dynamic programming algorithm mfold in terms of prediction accuracy on all tested structures. Expand
RnaPredict—An Evolutionary Algorithm for RNA Secondary Structure Prediction
TLDR
RnaPredict is shown to outperform the minimum free energy structures produced by mfold and has comparable performance when compared to suboptimal structures producedBy mfold. Expand
Using stacking-energies (INN and INN-HB) for improving the accuracy of RNA secondary structure prediction with an evolutionary algorithm - a comparison to known structures
  • A. Deschênes, K. Wiese
  • Physics, Computer Science
  • Proceedings of the Congress on Evolutionary…
  • 19 June 2004
TLDR
The accuracy of the predicted structures is compared to the known structures thus demonstrating the benefits of using stacking-energies in structure prediction and some other improvements to the EA are also discussed. Expand
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