Welcome to the ProbKnot Web Server

The ProbKnot server takes a sequence file of nucleic acids, either DNA or RNA, and predicts the secondary structure including pseudoknots. 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.

:
RNAstructure tools have been updated to version which includes several improvements.
Please contact us with any questions or issues regarding this update.

Select Sequence Input:

Select Sequence File:

- 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 Title: Sequence: (Example sequence has been displayed.)

AUGACUCUCU AAAUAGCAAU AUUUACCUUU GGAGGGAAAA GUUAUCAGGC AUGCACCUGG UAGCUAGUCU UUAAACCAAU AGAUUGCAUC GGUUUAAAAG GCAAGACCGU CAAAUUGCGG GAAAGGGGUC AACAGCCGUU CAGUACCAAG UCUCAGGGGA AACUUUGAGA UGGCCUUGCA AAGGGUAUGG UAAUAAGCUG ACGGACAUGG UCCUAACCAC GCAGCCAAGU CCUAAGUCAA CAGAUCUUCU GUUGAUAUGG AUGCAGUUCA CAGACUAAAU GUCGGUCGGG GAAGAUGUAU UCUUCUCAUA AGAUAUAGUC GGACCUCUCC UUAAUGGGAG CUAGCGGAUG AAGUGAUGCA ACACUGGAGC CGCUGGGAAC UAAUUUGUAU GCGAAAGUAU AUUGAUUAGU UUUGGAGUAC UCGUAAGGUA GCC

Select Nucleic Acid Type:

DNA:
RNA:

Select ProbKnot Options:

Default Data If a default value is left blank, the value is treated as if it was not changed at all. Iterations: Minimum Helix Length:

Designate Address to Email Results:

Address to Email Results:

RNAstructure

Web Servers for RNA Secondary Structure Prediction

Welcome to the ProbKnot Web Server

Select Sequence Input:

Select Nucleic Acid Type:

Select ProbKnot Options:

Designate Address to Email Results: