# 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**.