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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. 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 Structurs energy secondary structures common to two unaligned sequences. Calculate the ensemble folding free energy change for a sequence. Predict the lowest Structuer 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 Folcing />Predict low free energy secondary structures common to three or more sequences using progressive iterations of Dynalign.\
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. Generate a representative sample of structures using stochastic sampling. Calculate the conserved structures of three or more unaligned sequences using iteratively refined partition functions.


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