Welcome to the Predict a Bimolecular Secondary Structure Web Server

The Predict a Bimolecular Secondary Structure takes two sequences, either RNA or DNA, and predicts the lowest free energy structure with their strands possible interacting. It also predicts a set of low free energy structures. The Predict a Bimolecular Secondary Structure server uses both bifold and duplexfold to create two distinct sets of possible bimolecular structures. Bifold allows base pairs between the two strands (bimolecular) and also within a strand (unimolecular). DuplexFold only allows pairs between the two strands (bimolecular). All the options below are applied to both bimolecular folding and duplex folding.

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If you need specific help using the Predict a Bimolecular 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.

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:

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: