Welcome to the Mathews Lab RNAstructure Web Servers (original) (raw)
Secondary Structure Prediction:
- Predict a Secondary Structure
- Predict a Secondary Structure Common to Two Sequences
- Predict a Secondary Structure Common to Three or More Sequences
- Predict a Bimolecular Secondary Structure
Run a Specific Algorithm:
Generate all possible low free energy structures for a nucleic acid sequence.
Predict the lowest free energy structure for two interacting sequences, allowing intramolecular base pairs.
Perform a partition function calculation for two interacting nucleic acid sequences. Intramolecular pairs are not allowed.
Compare two structures using overlaid circular plots to emphasize pairing differences and pseudoknots.
Convert a CT-formatted structure into a dot bracket file.
Convert a dot bracket file into a CT file.
Draw the secondary structure of a strand of nucleic acids, with or without color annotation.
Predict the lowest free energy structure for two interacting sequences, not allowing intramolecular base pairs.
Calculate the lowest free energy secondary structures common to two unaligned sequences.
Calculate the folding free energy of structures in a CT file.
Calculate the ensemble folding free energy change for a sequence.
Predict the lowest free energy structure and a set of low free energy structures for a sequence.
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.
Predict low free energy secondary structures common to three or more sequences using progressive iterations of Dynalign.
Predict stability of hybridization and self-structure for a list of oligonucleotides.
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.
Perform a partition function calculation on a single sequence to calculate base pair probabilities.
Predict the common secondary structure, including base pair probabilities, for two unaligned sequences.
Generate secondary structures composed of base pairs with probabilities that exceed a specified threshold.
Predict a secondary structure of probable base pairs, which might include pseudoknots.
Remove pseudoknots from a structure.
Visualize partition function calculations of base pairing probabilities. (An external link to a server offered by the Daniel Aalberts lab.)
Calculate the sensitivity and positive predictive value (PPV) for a predicted as compared to the accepted structure.
Generate a representative sample of structures using stochastic sampling.
Calculate the conserved structures of three or more unaligned sequences using iteratively refined partition functions.