Welcome to the DuplexFold Web Server

The DuplexFold server predicts the lowest free energy structure for two interacting sequences, either RNA or DNA. The DuplexFold server only allows intermolecular base pairs and therefore does not allow formation of intramolecular pairs.

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.

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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.

Example sequences have been displayed.

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: GGGGGCGUAG CUCAGAuGGU AGAGCGCUCG CUUgGCgUGU GAGAGGUACC GGGAUCGaUA CCCGGCGCCU

Select Sequence 2:
Select Sequence File 2:
- 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 2 Title: Sequence 2: GGGGGCGUAG CUCAGAuGGU AGAGCGCUCG CUUgGCgUGU GAGAGGUACC GGGAUCGaUA CCCGGCGCCU

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:

RNAstructure

Web Servers for RNA Secondary Structure Prediction

Welcome to the DuplexFold Web Server

Select Sequence 1 Input:

Select Sequence 2:

Select Nucleic Acid Type:

Select DuplexFold Options:

Designate Address to Email Results: