Welcome to the Predict a Secondary Structure Web Server

The Predict a Secondary Structure server combines four separate prediction and analysis algorithms: calculating a partition function, predicting a maximum free energy (MFE) structure, finding structures with maximum expected accuracy, and pseudoknot prediction. This server takes a sequence, either RNA or DNA, and creates a highly probable, probability annotated group of secondary structures, starting with the lowest free energy structure and including others with varied probabilities of correctness. Other structures are included because the minimum free energy structure may not be the correct one. Note that if SHAPE constraints are specified, the SHAPE constraints are applied to the probability annotated structures. In addition, a second group of SHAPE constrained, SHAPE annotated structures will be generated. This SHAPE structure group is distinct from the probability annotated structure group, and is not probability annotated itself.

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If you need specific help using the Predict a Secondary Structure server, please click here.

Select Sequence Input:

- OR -
Enter your sequence title and content below (replaces upload if present).
Please enter nucleotides only, no headers or comments in content.
Valid nucleotides are A, C, G, T, U, and X (unknown nucleotide). Lower case nucleotides are forced single stranded in calculation.




Select Nucleic Acid Type:




Select Predict a Secondary Structure Options:

If a default value is left blank, the value is treated as if it was not changed at all.



Note that in order to use SHAPE intercept and/or SHAPE slope, a SHAPE constraints file must be specified. If a value is given for intercept or slope without an accompanying constraints file, the intercept or slope value is not used in calculation.


Specify the minimum and maximum probabilities to show on the dot plot.
If a specified probability is out of range, it is ignored.



Designate Address to Email Results: