| Name: |
AllSub |
| Type: |
Text Interface |
| Location: |
RNAstructure/AllSub |
| Description: |
Generate a group of suboptimal structures. |
| To Build: |
In the RNAstructure/ directory, type "make AllSub." |
| Name: |
bifold |
| Type: |
Text Interface |
| Location: |
RNAstructure/bifold |
| Description: |
Do bimolecular secondary structure prediction by free energy minimization, allowing intramolecular pairs. |
| To Build: |
In the RNAstructure/ directory, type "make bifold." |
| Name: |
bipartition |
| Type: |
Text Interface |
| Location: |
RNAstructure/bipartition |
| Description: |
Do a bimolecular partition function with two sequences, not allowing intramolecular pairs. |
| To Build: |
In the RNAstructure/ directory, type "make bipartition." |
| Name: |
CircleCompare |
| Type: |
Text Interface |
| Location: |
RNAstructure/CircleCompare |
| Description: |
Compare two structures by creating a postscript file, overlaying their backbones on a circle. |
| To Build: |
In the RNAstructure/ directory, type "make CircleCompare." |
| Name: |
ct2dot |
| Type: |
Text Interface |
| Location: |
RNAstructure/ct2dot |
| Description: |
Convert a CT structure file to a dot bracket structure file. |
| To Build: |
In the RNAstructure/ directory, type "make ct2dot." |
| Name: |
dot2ct |
| Type: |
Text Interface |
| Location: |
RNAstructure/dot2ct |
| Description: |
Convert a dot bracket structure file to a CT structure file. |
| To Build: |
In the RNAstructure/ directory, type "make dot2ct." |
| Name: |
draw |
| Type: |
Text Interface |
| Location: |
RNAstructure/draw |
| Description: |
Draw a Postscript image of a structure. |
| To Build: |
In the RNAstructure/ directory, type "make draw." |
| Name: |
DuplexFold |
| Type: |
Text Interface |
| Location: |
RNAstructure/DuplexFold |
| Description: |
Do bimolecular secondary structure prediction by free energy minimization, with intramolecular pairs forbidden. |
| To Build: |
In the RNAstructure/ directory, type "make DuplexFold." |
| Name: |
dynalign |
| Type: |
Text Interface |
| Location: |
RNAstructure/dynalign |
| Description: |
Find the common secondary structure for two sequences. |
| To Build: |
In the RNAstructure/ directory, type "make dynalign." |
| Name: |
dynalign-smp |
| Type: |
Text Interface |
| Location: |
RNAstructure/dynalign |
| Description: |
Find the common secondary structure for two sequences. This program can be run in a parallel SMP environment. |
| To Build: |
In the RNAstructure/ directory, type "make dynalign-smp." |
| Name: |
DynalignDotPlot |
| Type: |
Text Interface |
| Location: |
RNAstructure/DotPlots |
| Description: |
Create a Postscript dot plot of pairing energies from a Dynalign save file. |
| To Build: |
In the RNAstructure/ directory, type "make DynalignDotPlot." |
| Name: |
efn2 |
| Type: |
Text Interface |
| Location: |
RNAstructure/efn2 |
| Description: |
Calculate the folding free energy change of structures. |
| To Build: |
In the RNAstructure/ directory, type "make efn2." |
| Name: |
EnergyPlot |
| Type: |
Text Interface |
| Location: |
RNAstructure/DotPlots |
| Description: |
Create a Postscript dot plot of pairing energies from a folding save file. |
| To Build: |
In the RNAstructure/ directory, type "make EnergyPlot." |
| Name: |
EnsembleEnergy |
| Type: |
Text Interface |
| Location: |
RNAstructure/EnsembleEnergy |
| Description: |
Calculate the ensemble folding free energy change for a sequence. |
| To Build: |
In the RNAstructure/ directory, type "make EnsembleEnergy." |
| Name: |
Fold |
| Type: |
Text Interface |
| Location: |
RNAstructure/fold |
| Description: |
Fold a single sequence into its lowest free energy conformation. |
| To Build: |
In the RNAstructure/ directory, type "make Fold." |
| Name: |
Java Cross-Platform Interface |
| Type: |
GUI Interface |
| Location: |
RNAstructure/java_interface |
| Description: |
A cross-platform GUI for RNAstructure. |
| To Build: |
In the RNAstructure/java_interface directory, type "make." |
| Name: |
MaxExpect |
| Type: |
Text Interface |
| Location: |
RNAstructure/MaxExpect |
| Description: |
Predict maximum expected accuracy structures. |
| To Build: |
In the RNAstructure/ directory, type "make MaxExpect." |
| Name: |
multilign |
| Type: |
Text Interface |
| Location: |
RNAstructure/multilign |
| Description: |
Find the structures common for more than two homologous sequences. |
| To Build: |
In the RNAstructure/ directory, type "make multilign." |
| Name: |
multilign-smp |
| Type: |
Text Interface |
| Location: |
RNAstructure/multilign |
| Description: |
Find the structures common for more than two homologous sequences. This program can be run in a parallel SMP environment. |
| To Build: |
In the RNAstructure/ directory, type "make multilign-smp." |
| Name: |
NAPSS |
| Type: |
Text Interface |
| Location: |
RNAstructure/napss |
| Description: |
Use NMR data to assist in predicting secondary structure. |
| To Build: |
In the RNAstructure/ directory, type "make NAPSS." |
| Name: |
oligoscreen |
| Type: |
Text Interface |
| Location: |
RNAstructure/oligoscreen |
| Description: |
Calculate thermodynamic properties of a set of oligonucleotides. |
| To Build: |
In the RNAstructure/ directory, type "make oligoscreen." |
| Name: |
OligoWalk |
| Type: |
Text Interface |
| Location: |
RNAstructure/OligoWalk |
| Description: |
Calculate affinity of target RNA binding by oligomers complementary to a specified RNA target. |
| To Build: |
In the RNAstructure/ directory, type "make OligoWalk." |
| Name: |
partition |
| Type: |
Text Interface |
| Location: |
RNAstructure/pfunction |
| Description: |
Calculate the partition function of a sequence. |
| To Build: |
In the RNAstructure/ directory, type "make partition." |
| Name: |
PARTS |
| Type: |
Text Interface |
| Location: |
RNAstructure/PARTS |
| Description: |
Calculate common structures and pairing probabilities for two unaligned sequences. |
| To Build: |
In the RNAstructure/ directory, type "make PARTS." |
| Name: |
ProbabilityPlot |
| Type: |
Text Interface |
| Location: |
RNAstructure/DotPlots |
| Description: |
Create a Postscript dot plot of base pair probabilities from a partition function save file. |
| To Build: |
In the RNAstructure/ directory, type "make ProbabilityPlot." |
| Name: |
ProbablePair |
| Type: |
Text Interface |
| Location: |
RNAstructure/ProbablePair |
| Description: |
Output structures composed of pairs with pairing probabilities that exceed one or more specific probability thresholds. |
| To Build: |
In the RNAstructure/ directory, type "make ProbablePair." |
| Name: |
ProbKnot |
| Type: |
Text Interface |
| Location: |
RNAstructure/ProbKnot |
| Description: |
Predict secndary structures that may contain pseudoknots. |
| To Build: |
In the RNAstructure/ directory, type "make ProbKnot." |
| Name: |
refold |
| Type: |
Text Interface |
| Location: |
RNAstructure/refold |
| Description: |
Refold a previously folded sequence. |
| To Build: |
In the RNAstructure/ directory, type "make refold." |
| Name: |
RemovePseudoknots |
| Type: |
Text Interface |
| Location: |
RNAstructure/RemovePseudoknots |
| Description: |
Remove as few pairs as possible to transform a pseudoknotted structure into a non-pseudoknotted one. |
| To Build: |
In the RNAstructure/ directory, type "make RemovePseudoknots." |
| Name: |
scorer |
| Type: |
Text Interface |
| Location: |
RNAstructure/scorer |
| Description: |
Score a predicted structure against an accepted one. |
| To Build: |
In the RNAstructure/ directory, type "make scorer." |
| Name: |
stochastic |
| Type: |
Text Interface |
| Location: |
RNAstructure/stochastic |
| Description: |
Sample structures from the Boltzmann ensemble. |
| To Build: |
In the RNAstructure/ directory, type "make stochastic." |
| Name: |
TurboFold |
| Type: |
Text Interface |
| Location: |
RNAstructure/TurboFold |
| Description: |
Find the structures common for more than two homologous sequences, using base pairing probabilities. |
| To Build: |
In the RNAstructure/ directory, type "make TurboFold." |
| Name: |
TurboFold-smp |
| Type: |
Text Interface |
| Location: |
RNAstructure/TurboFold |
| Description: |
Find the structures common for more than two homologous sequences, using base pairing probabilities. This program can be run in a parallel SMP environment. |
| To Build: |
In the RNAstructure/ directory, type "make TurboFold-smp." |
| Name: |
Windows Native Interface |
| Type: |
GUI Interface |
| Location: |
RNAstructure/Windows_interface_deprecated |
| Description: |
A natively compiled Windows GUI for RNAstructure. |
| To Build: |
TODO? |
| Name: |
Windows Text Interfaces |
| Type: |
Text Interface |
| Location: |
RNAstructure/Windows_text_interfaces |
| Description: |
Natively compiled Windows text interfaces for RNAstructure. |
| To Build: |
TODO? |
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