KnotSeeker: Heuristic pseudoknot detection in long RNA sequences

KnotSeeker is a heuristic method for the detection of pseudoknots in RNA sequences as a preliminary step for structure prediction. It uses a hybrid sequence matching and free energy minimization approach.

The maximum sequence length limit is set to 1000 bases for online submission. See the manual for more information on input and output format. If you want to run KnotSeeker on your local machine, feel free to download the code here.

You might like to try DotKnot, the more versatile and lovingly maintained successor of KnotSeeker.