Welcome to the Predict a Bimolecular Secondary Structure Web Server

The Predict a Bimolecular Secondary Structure folds two sequences, either RNA or DNA, into their lowest hybrid free energy conformation. The Predict a Bimolecular Secondary Structure server combines the capabilities of bimolecular folding and duplex folding to create two distinct sets of possible bimolecular structures. All the options below are applied to both bimolecular folding and duplex folding. Note that if an error is encountered in bimolecular folding, it may still be possible to fold one or both component sequences independently without errors.

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

February 14, 2018:
RNAstructure tools have been updated to version 6.0.1 which includes several improvements.
Please contact us with any questions or issues regarding this update.

Click here to add an example sequence to both sequence boxes.

Select Sequence 1 Input:

Select Sequence File 1:

- 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 1 Title: Sequence 1:

Select Sequence 2:

Select Sequence File 2:

Sequence 2 Title: Sequence 2:

Select Nucleic Acid Type:

DNA:
RNA:

Select Predict a Bimolecular Secondary Structure Options:

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

Designate Address to Email Results:

Address to Email Results: