Welcome to the DuplexFold Web Server

The DuplexFold server is similar to the Bimolecular Fold server; it folds two sequences, either RNA or DNA, into their lowest hybrid free energy conformation. The Bimolecular Fold server allows formation of intramolecular pairs if desired, but the DuplexFold server does not allow formation of intramolecular pairs. Note that if an error is encountered in duplex folding, it may still be possible to fold one or both component sequences independently without errors.

If you plan to leave this page while waiting for calculations to complete, please make sure you have entered a valid email address below. Leaving this page without entering a valid email address will render results inaccessible.

If you need specific help using the DuplexFold 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 DuplexFold 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: