Secondary Structure Prediction:
Run a Specific Algorithm:
 AllSub
 Generate all possible low free energy structures for a nucleic acid sequence.
 bifold
 Predict the lowest free energy structure for two interacting sequences, allowing intramolecular base pairs.
 bipartition
 Perform a partition function calculation for two interacting nucleic acid sequences. Intramolecular pairs are not allowed.
 CircleCompare
 Compare two structures using overlaid circular plots to emphasize pairing differences and pseudoknots.
 ct2dot
 Convert a CTformatted structure into a dot bracket file.
 dot2ct
 Convert a dot bracket file into a CT file.
 draw
 Draw the secondary structure of a strand of nucleic acids, with or without color annotation.
 DuplexFold
 Predict the lowest free energy structure for two interacting sequences, not allowing intramolecular base pairs.
 Dynalign
 Calculate the lowest free energy secondary structures common to two unaligned sequences.
 efn2
 Calculate the folding free energy of structures in a CT file.
 EnsembleEnergy
 Calculate the ensemble folding free energy change for a sequence.
 Fold
 Predict the lowest free energy structure and a set of low free energy structures for a sequence.
 MaxExpect
 Generate a structure or structures composed of highly probable base pairs. This is an alternative method for structure prediction that may have higher fidelity in structure prediction.
 Multilign
 Predict low free energy secondary structures common to three or more sequences using progressive iterations of Dynalign.
 oligoscreen
 Predict stability of hybridization and selfstructure for a list of oligonucleotides.
 OligoWalk for siRNA design

Design efficient siRNAs for a given miRNA target.
Please note that this is an independent server, so its format is slightly different from the rest of the servers.
 partition
 Perform a partition function calculation on a single sequence to calculate base pair probabilities.
 PARTS
 Predict the common secondary structure, including base pair probabilities, for two unaligned sequences.
 ProbablePair
 Generate secondary structures composed of base pairs with probabilities that exceed a specified threshold.
 ProbKnot
 Predict a secondary structure of probable base pairs, which might include pseudoknots.
 RemovePseudoknots
 Remove pseudoknots from a structure.
 RNAbows
 Visualize partition function calculations of base pairing probabilities. (An external link to a server offered by the Daniel Aalberts lab.)
 scorer
 Calculate the sensitivity and positive predictive value (PPV) for a predicted as compared to the accepted structure.
 stochastic
 Generate a representative sample of structures using stochastic sampling.
 TurboFold
 Calculate the conserved structures of three or more unaligned sequences using iteratively refined partition functions.