CONTRAfold: RNA secondary structure prediction without physics-based models

RNA secondary structure prediction and runtime optimization

1. Background RNA secondary structure Pseudoknots Non-coding RNA 2. CONTRAfold: Probabilistic RNA folding Overview of the algorithm Details of the algorithm Performance of CONTRAfold 3. Other RNA folding methods: Physics-based models and Stochastic Context Free Grammars Physics-based models Stochastic Context Free Grammars Advantages of CONTRAfold over these other approaches 4. How RNA folding ...

Semi-Supervised CONTRAfold for RNA Secondary Structure Prediction: A Maximum Entropy Approach

A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more.

The standard approach for single-sequence RNA secondary structure prediction uses a nearest-neighbor thermodynamic model with several thousand experimentally determined energy parameters. An attractive alternative is to use statistical approaches with parameters estimated from growing databases of structural RNAs. Good results have been reported for discriminative statistical methods using comp...

A max-margin model for efficient simultaneous alignment and folding of RNA sequences

MOTIVATION The need for accurate and efficient tools for computational RNA structure analysis has become increasingly apparent over the last several years: RNA folding algorithms underlie numerous applications in bioinformatics, ranging from microarray probe selection to de novo non-coding RNA gene prediction. In this work, we present RAF (RNA Alignment and Folding), an efficient algorithm for ...

Recent Developments in RNA Secondary Structure Prediction

Here we discuss recent developments in predicting RNA secondary structure, giving an overview of methods used, including energy minimization and Boltzmann sampling, a probabilistic approach, and the use of fragment libraries generated from high resolution three-dimensional RNA crystal structures. An example for each of these three methods is discussed in detail (namely Sfold, CONTRAfold and MC-...