Pseudoknot Types
H-type pseudoknots
DotKnot includes the class of recursive H-type pseudoknots where one of the pseudoknot stems may be interrupted by bulge loops or internal loops. All three pseudoknot loops are allowed to contain recursive secondary structures.
DotKnot uses pseudoknot loop entropy parameters published by Song Cao and Shi-Jie Chen in 2006 and 2009. For a description of the DotKnot algorithm and more details, see our paper.
Kissing hairpins
The user can choose whether kissing hairpins are included in addition to H-type pseudoknots in the prediction by DotKnot. If kissing hairpins are included, the maximum sequence length limit is set to 400 bases for online submission.
