DotKnot: pseudoknot prediction including kissing hairpins

dotplot DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence.

DotKnot extracts stem regions from the secondary structure probability dot plot calculated by RNAfold. Recursive H-type pseudoknots and intramolecular kissing hairpins are constructed and their presence in the sequence is verified. The detected pseudoknots can then be further analysed using bioinformatics or laboratory techniques.

For online submission, the maximum sequence length limit is set to 1000 bases for H-type pseudoknot prediction and to 400 bases if kissing hairpins are included.

See the manual for more information on input and output format.

If you want to run DotKnot on your local machine for longer sequence, you can download the current version: DotKnot_1.3.2.tar.gz.

Previous versions are available from the archive.


Include kissing hairpins ?
Show best local pseudoknots ?
Show global structure ?