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Pseudoknot Removal Server

Please do not link this web address!
For stable links, please refer to or

K2N: a service to get from knotted to nested RNA structures. This site provides access to a variety of methods for pseudoknot removal.




  • Small set of pseudoknotted base pairs (bpseq) (ct)
  • Larger set of pseudoknotted base pairs (bpseq) (ct)



If you use our method, please cite:
Sandra Smit, Kristian Rother, Jaap Heringa, and Rob Knight.
From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal.
RNA (2008) 14(3):410-416.
[Online supplementary material]


This code is no longer actively maintained. Please, email me if you have any questions.


Input base pairs

Paste in a set of base pairs in bp or ct format:

Or Upload a file with base pairs in bp or ct format:

Input Format

Removal method
(explain the different methods)

 EG - Elimination, gain
 EC - Elimination, conflicts
 IO - Incremental, order
 IL - Incremental, length
 IR - Incremental, range
 OA - All optimal solutions
 OSR - Single optimal solution picked randomly
 OSP - Single optimal solution picked by property

Output format

 Report removed pairs



The Pseudoknot Removal web server was developed by Sandra Smit, Kristian Rother, Jaap Heringa, and Rob Knight

(c) IBIVU 2021. If you are experiencing problems with the site, please contact the webmaster.