List of RNA Structure Prediction Software - Single Sequence Secondary Structure Prediction

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
Notes

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