AntaRNA - Multi-obj. Sequence Design

AntaRNA is an Ant-Colony Optimization based tool which solves the RNA inverse folding problem. It designs RNA sequences which satisfy a set of constraints made by the user. The realized multi-objective optimization allows to introduce structure, sequence and GC-content constraints.

For articles describing the tool and webserver refer to the reference section below. Please cite us when using our tools.
For more information check the help page.

Try AntaRNA with these examples:

Nested tRNA structure (input|result)
Crossing pseudoknot (input|result)
SECIS block design (input|result)

Constraints

Structure constraint (dot-bracket notation)

Sequence constraint [optional]

Constraint visualization

Explicit structure constraints are given in white, invalid base pairs in red, block constraints colored. Visualization done with forna

Targeted GC-content [0..1]:

Maximum for uniform distribution sampling:

Variance for normal distribution sampling:

Allow GU base pairs:

Allow pseudoknots (fixed AntaRNA parameters)

Output

Number of sequences:

Method

[+] Energy [-] Energy

Folding temperature:

[+] AntaRNA [-] AntaRNA

Max. terrain resets:

Convergence counts:

Ant termination criterion:

Probability weight alpha:

Probability weight beta:

Pheromone evaporation rate:

Constraint weight structure:

Constraint weight sequence:

Constraint weight GC-value:

Random seed:

Description:

Your Email:

(optional)
(optional)

When using AntaRNA please cite :

Robert Kleinkauf, Martin Mann and Rolf Backofen
AntaRNA - Ant Colony Based RNA Sequence Design
Bioinformatics, 31(19), pages 3114-3121, 2015.
Robert Kleinkauf, Torsten Houwaart, Rolf Backofen, and Martin Mann
AntaRNA - multi-objective inverse folding of pseudoknot RNA using ant-colony optimization
BMC Bioinformatics, 16(1), pages 1-7, 2015.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with AntaRNA version 1.1.2 using Vienna RNA package 2.1.8 or pKiss (2014-03-17)

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching