Pseudoknot Removal Server

K2N: a service to get from knotted to nested RNA structures. This site provides access to a variety of methods for pseudoknot removal. Documentation: Background and methods Information on the accepted data formats Examples: Small set of pseudoknotted base pairs (bpseq) (ct) Larger set of pseudoknotted base pairs (bpseq) (ct) Code: Full source code available in the PyCogent library Standalone implementation Reference: 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 [Online supplementary material] Maintenance: This code is no longer actively maintained.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 Bpseq format Ct 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 Same as input Bpseq format Ct format Vienna format  Report removed pairs
The Pseudoknot Removal web server was developed by Sandra Smit, Kristian Rother, Jaap Heringa, and Rob Knight