IPknot: IP-based prediction of RNA pseudoKNOTs

Version 2.2.1
Last modified: 2023-03-01

Overview

The IPknot++ web server is an improved version of the IPknot web server, which provides services for predicting RNA secondary structures including a wide class of pseudoknots. The IPknot++ web server can perform RNA secondary structure prediction including pseudoknots for very long sequences by employing the LinearPartition model. IPknot can also predict the consensus secondary structure when a multiple alignment of RNA sequences is given. IPknot runs fast and predicts the maximum expected accuracy (MEA) structure using integer programming (IP) with threshold cut. Detailed instructions for use are found here.

Interface

Enter your RNA sequence (FASTA format, or only a sequence in 5'–3' direction) or alignment (CLUSTAL W, or multiple FASTA format) here.

Or upload your FASTA/CLUSTAL W/multiple FASTA format file:

Options

You can adjust several parameters. If you do not change the parameters, the default values will be submitted to the server.

Choose a level for prediction:
Choose a scoring model:
Refine parameters?
Use pseudo-expected accuracy
OR
Enter a positive weight for true base pairs at each level:
Level 1 Level 2 Level 3

Downloads

The C++ source codes can be used as a standalone version of IPknot.

If you have any questions, please contact Yuki Kato, Kengo Sato.

Graduate School of Medicine, Osaka University, Japan
School of System Design and Technology, Tokyo Denki University, Japan