Name
|
Description |
Institution |
Links |
References
|
European Nucleotide Archive
|
Secondary structure prediction based on generalized centroid estimator |
no |
sourcecode webserver |
[1]
|
GenBank
|
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 |
[2]
|
DNA Data Bank of Japan
|
Secondary structure prediction method based on placement of helices allowing complex pseudoknots. |
yes |
webserver |
[3]
|
KineFold
|
Folding kinetics of RNA sequences including pseudoknots by including an implementation of the partition function for knots. |
yes |
linuxbinary, webserver |
[4][5]
|
Mfold
|
MFE RNA structure prediction algorithm. |
no |
sourcecode, webserver |
[6]
|
Pknots
|
A dynamic programming algorithm for optimal RNA pseudoknot prediction using the nearest neighbour energy model. |
yes |
sourcecode |
[7]
|
PknotsRG
|
A dynamic programming algorithm for the prediction of a restricted class of RNA pseudoknots. |
yes |
sourcecode, webserver |
[8]
|
|
RNAfold
|
MFE RNA structure prediction algorithm. Includes an implementation of the partition function for computing basepair probabilities and circular RNA folding. |
no |
sourcecode, webserver |
[6][9][10][11][12][13]
|
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 |
[14][15]
|
RNAstructure
|
A program to predict lowest free energy structures and base pair probabilities for RNA or DNA sequences. 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. |
no |
source & binaries |
[16][17]
|
Sfold
|
Statistical sampling of all possible structures. The sampling is weighted by partition function probabilities. |
no |
webserver |
[18][19][20][21]
|
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 |
[22]
|
*Knots: Pseudoknot prediction, <yes|no>.
|