Single Sequence Secondary Structure Prediction
Name | Description | Knots |
Links | References |
---|---|---|---|---|
CentroidFold | Secondary structure prediction based on generalized centroid estimator | no | sourcecode webserver | |
CentroidHomfold | Secondary structure prediction by using homologous sequence information | no | sourcecode webserver | |
Context Fold | An RNA secondary structure prediction software which applies feature-rich trained scoring models. | no | sourcecode webserver | |
CONTRAfold | Secondary structure prediction method based on conditional log-linear models (CLLMs), a flexible class of probabilistic models which generalize upon SCFGs by using discriminative training and feature-rich scoring. | no | sourcecode webserver | |
CyloFold | Secondary structure prediction method based on placement of helices allowing complex pseudoknots. | yes | webserver | |
KineFold | Folding kinetics of RNA sequences including pseudoknots by including an implementation of the partition function for knots. | yes | linuxbinary, webserver | |
Mfold | MFE (Minimum Free Energy) RNA structure prediction algorithm. | no | sourcecode, webserver | |
Pknots | A dynamic programming algorithm for optimal RNA pseudoknot prediction using the nearest neighbour energy model. | yes | sourcecode | |
PknotsRG | A dynamic programming algorithm for the prediction of a restricted class of RNA pseudoknots. | yes | sourcecode, webserver | |
RNA123 | Secondary structure prediction via thermodynamic-based folding algorithms and novel structure-based sequence alignment specific for RNA. | yes | webserver | |
RNAfold | MFE RNA structure prediction algorithm. Includes an implementation of the partition function for computing basepair probabilities and circular RNA folding. | no | sourcecode, webserver | |
RNAshapes | MFE RNA structure prediction based on abstract shapes. Shape abstraction retains adjacency and nesting of structural features, but disregards helix lengths, thus reduces the number of suboptimal solutions without losing significant information. Furthermore, shapes represent classes of structures for which probabilities based on Boltzmann-weighted energies can be computed. | no | source & binaries, webserver | |
RNAstructure | A program to predict lowest free energy structures and base pair probabilities for RNA or DNA sequences. Programs are also available to predict Maximum Expected Accuracy structures and these can include pseudoknots. Structure prediction can be constrained using experimental data, including SHAPE, enzymatic cleavage, and chemical modification accessibility. Graphical user interfaces are available for Windows and for Mac OS-X/Linux. Programs are also available for use with Unix-style text interfaces. Additionally, a C++ class library is available. | yes | source & binaries | |
Sfold | Statistical sampling of all possible structures. The sampling is weighted by partition function probabilities. | no | webserver | |
UNAFold | The UNAFold software package is an integrated collection of programs that simulate folding, hybridization, and melting pathways for one or two single-stranded nucleic acid sequences. | no | sourcecode | |
Crumple | Crumple is simple, cleanly written software for producing the full set of possible secondary structures for a single sequence, given optional constraints. | no | sourcecode | |
Sliding Windows & Assembly | Sliding windows and assembly is a tool chain for folding long series of similar hairpins. | no | sourcecode | |
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