Welcome to the ProbKnot Web Server

The ProbKnot server takes a sequence file of nucleic acids, either DNA or RNA, and predicts the presence of pseudoknots in its folded configuration. Note that increasing the number of calculation iterations may be helpful in increasing accuracy. Note also that if a pseudoknot-containing structure is predicted, it will be displayed as a circular structure. If the predicted structure does not contain pseudoknots, it will be displayed as a radial structure.

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 ProbKnot 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.

Select Sequence 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 Nucleic Acid Type:

Select ProbKnot Options:

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

Designate Address to Email Results: