IPknot: IP-based prediction of RNA pseudoKNOTs

Version 2.2.1
Last modified: 2023-03-01

Overview

The IPknot web server provides services for predicting RNA secondary structures including a wide class of pseudoknots. 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. The IP problem is solved by GNU Linear Programming Kit (GLPK). Detailed instructions for use are found here.

Note: An improved version of this server, the IPknot++ web server, is available. We recommend to use the IPknot++ web server instead of this server except for special reasons such as backward compatibility.

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?
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.
The Perl template program accesses several of the web services and parses the output.

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