Welcome to the Predict a Secondary Structure Web Server

The Predict a Secondary Structure server combines three secondary structure prediction algorithms: predicting a minimum free energy (MFE) structure, the maximum expected accuracy (MEA) structure, and the probknot structure. The input is an RNA or DNA sequence. The three predictions represent alternative hypotheses for the secondary structure. The MFE structure is the structure predicted to be most probable at equilibrium. The MEA structure is composed of the most probable base pairs, and the probknot structure can predict pseudoknotted base pairs. All predicted structures are color-annotated by base pairing probabilities. Within a predicted structure, the higher probability pairs are on average more likely to be correct predictions.

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

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RNAstructure tools have been updated to version which includes several improvements.
Please contact us with any questions or issues regarding this update.

Select Sequence Input:

Select Sequence File:

- 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.

Sequence Title: Sequence: (Example sequence has been displayed.)

GGGGGCGUAG CUCAGAuGGU AGAGCGCUCG CUUgGCgUGU GAGAGGUACC GGGAUCGaUA CCCGGCGCCU CCACCA

Select Nucleic Acid Type:

DNA:
RNA:

Select Predict a Secondary Structure Options:

Default Data If a default value is left blank, the value is treated as if it was not changed at all. Temperature (K): Maximum Loop Size: Maximum % Energy Difference (MFE, MEA): Maximum Number of Structures (MFE, MEA): Window Size (MFE, MEA): Gamma (MEA): Iterations (Pseudoknot Prediction): Minimum Helix Length (Pseudoknot Prediction):

Optional Data Select Folding Constraints File:

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. Select SHAPE Constraints File: SHAPE Intercept: SHAPE Slope:

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

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Address to Email Results:

RNAstructure

Web Servers for RNA Secondary Structure Prediction

Welcome to the Predict a Secondary Structure Web Server

Select Sequence Input:

Select Nucleic Acid Type:

Select Predict a Secondary Structure Options:

Designate Address to Email Results: