| Directory |
Description |
| AllSub |
Generate a group of suboptimal structures |
| bifold |
Bimolecular folding |
| bipartition |
Bimolecular partition function for predicting pair probabilities |
| CircleCompare |
Compare
two structures for the same sequence, with the nucleic acid backbone
arranged around a circle to facilitate easy comparisons |
| ct2dot |
Convert CT structure notation to dot bracket structure notation |
| design | Find an RNA (or DNA) sequence that is expected to fold into a given structure. |
| dot2ct |
Convert dot bracket structure notation to CT structure notation |
| DotPlots |
Creates three separate interfaces that can make different dot plot types |
| draw |
Generate Postscript images of secondary structures |
| DuplexFold |
Bimolecular folding without intramolecular pairs |
| dynalign |
Predict the lowest free energy structure common to two sequences |
| efn2 |
Predict folding free energy change of a given structure |
| EnsembleEnergy |
Predict the energy of a structure ensemble. |
| fold |
Single sequence secondary structure prediction by free energy minimization |
| MaxExpect |
Secondary structure prediction by maximizing expected accuracy |
| multilign |
Predict the lowest free energy structure common to more than two sequences |
| napss |
Use NMR data to improve the prediction of an RNA secondary structure |
| oligoscreen |
Screen a set of oligonuceotides for hybridization stability and self-structure |
| oligowalk |
Calculate thermodynamic features of sense-antisense hybridization and predict free energy changes of oligo binding to target RNA |
| PARTS |
Predict pair probabilities for folding of two sequences to a common structure |
| pfunction |
Partition function calculation of base pairing probabilities |
| ProbablePair |
Generate structures composed of only highly probable pairs as determined by a threshold |
| ProbKnot |
Predict pseudoknots for a single sequence |
| refold |
Refold a previously folded structure |
| RemovePseudoknots |
Remove pseudoknots from a structure |
| Windows_text_interfaces |
Visual Studio Project files for editing and building the Text interfaces on Windows |
| scorer |
Calculate sensitivity and positive predictive value for two structures being compared |
| stochastic |
Stochastic sampling from the Boltzman ensemble |
| TurboFold |
Predict the lowest free energy structure common to more than two sequences, using base pairing probabilities. |
