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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Select Sequence 1 Input:

- 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.




Select Sequence 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.




Select Nucleic Acid Type:




Select Predict a Bimolecular Secondary Structure Options:

If a default value is left blank, the value is treated as if it was not changed at all.



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