RNA inverse folding software tools | Synthetic biology
RNA sequence design is studied at least as long as the classical folding problem. While for the latter the functional fold of an RNA molecule is to be found, inverse folding tries to identify RNA sequences that fold into a function-specific target structure. In combination with…
Desktop app
RNA-ensign RNA-ensign

RNA-ensign

Designs RNA sequences folding into target secondary structures. RNA-ensign uses…

Designs RNA sequences folding into target secondary structures. RNA-ensign uses an ensemble-based energy optimization method based on RNAmutants software. Instead of taking a progressive adaptive…

Web app
Desktop app
Evolutionary RNA… Evolutionary RNA Designer

ERD Evolutionary RNA Designer

Designs sequences that fold into a given target RNA secondary structure, i.e.…

Designs sequences that fold into a given target RNA secondary structure, i.e. whose minimum free energy (MFE) structure is the target structure. ERD is an evolutionary algorithm for RNA design…

Web app
incaRNAfbinv incaRNAfbinv

incaRNAfbinv

A merge between RNAfbinv and incaRNAtion. incaRNAfbinv offers sequence design…

A merge between RNAfbinv and incaRNAtion. incaRNAfbinv offers sequence design solutions that to the best of our knowledge are not available in neither the most recently published programs for RNA…

Desktop app
Web app
A A A ViennaRNA ViennaRNA

ViennaRNA

A widely used collection of programs for thermodynamic RNA secondary structure…

A widely used collection of programs for thermodynamic RNA secondary structure prediction. Over the years, many additional tools have been developed building on the core programs of the package to…

Desktop app
Web app
Ant assembled RNA Ant assembled RNA

antaRNA Ant assembled RNA

Compiles RNA sequences for a given structure that comply in addition with an…

Compiles RNA sequences for a given structure that comply in addition with an adjustable full range objective GCcontent distribution, specific sequence constraints and additional fuzzy structure…

Desktop app
IncaRNAtion IncaRNAtion

IncaRNAtion

An algorithm to design RNA sequences folding into target secondary structures…

An algorithm to design RNA sequences folding into target secondary structures with a predefined nucleotide distribution. IncaRNAtion uses a global sampling approach and weighted sampling techniques.

Web app
RNA-Redesign RNA-Redesign

RNA-Redesign

An online 3D design tool for RNA. This resource utilizes fixed-backbone design…

An online 3D design tool for RNA. This resource utilizes fixed-backbone design to optimize the sequence identity and nucleobase conformations of an RNA to match a desired backbone, analogous to…

Desktop app
RNAexinv RNAexinv

RNAexinv

An interactive java application that performs RNA sequence design, constrained…

An interactive java application that performs RNA sequence design, constrained to yield a specific RNA shape and physical attributes. RNAexinv is an extended inverse RNA folding program with the…

Desktop app
RNAfbinv RNAfbinv

RNAfbinv

An interactive java application that performs RNA sequence design, constrained…

An interactive java application that performs RNA sequence design, constrained to yield a specific RNA shape and physical attributes. RNAfbinv is an extension of the RNAexinv inverse folding program…

Desktop app
Frnakenstein Frnakenstein

Frnakenstein

A python implementation of a genetic algorithm for inverse RNA folding.…

A python implementation of a genetic algorithm for inverse RNA folding. Frnakenstein allows a combination of the predicted minimum free energy structure and the computed Boltzmann distribution over…

Desktop app
Web app
INFO-RNA INFO-RNA

INFO-RNA

A web server for designing RNA sequences that fold into a user given secondary…

A web server for designing RNA sequences that fold into a user given secondary structure. Furthermore, constraints on the sequence can be specified, e.g. one can restrict sequence positions to a…

Desktop app
Multi-Objective… Multi-Objective DEsign of Nucleic Acids

MODENA Multi-Objective DEsign of Nucleic Acids

An RNA inverse folding program based on multi-objective genetic algorithm.…

An RNA inverse folding program based on multi-objective genetic algorithm. MODENA explores the approximate set of weak Pareto optimal solutions in the objective function space of 2 objective…

Desktop app
Web app
RNA Inverse Folding RNA Inverse Folding

RNAiFold RNA Inverse Folding

A website that provides public access to the CPdesign and LNSdesign algorithms…

A website that provides public access to the CPdesign and LNSdesign algorithms for solving the RNA inverse folding problem. RNAiFold 2.0 is a complete overhaul of RNAiFold 1.0, rewritten from the now…

Web app
Mfold Mfold

Mfold

Provides easy access to RNA and DNA folding and hybridization software to the…

Provides easy access to RNA and DNA folding and hybridization software to the scientific community at large. Detailed output, in the form of structure plots with or without reliability information,…

Desktop app
Web app
NUPACK NUPACK

NUPACK

A growing software suite for the analysis and design of nucleic acid systems.…

A growing software suite for the analysis and design of nucleic acid systems. NUPACK enables thermodynamic analysis of dilute solutions of interacting nucleic acid strands and sequence design for…

Web app
RNA Designer RNA Designer

RNA Designer

Takes as input a secondary structure description and outputs an RNA strand that…

Takes as input a secondary structure description and outputs an RNA strand that is predicted to fold to that secondary structure. RNA Designer can be used to design RNA molecules with certain…

Desktop app
RNAdesign RNAdesign

RNAdesign

A user-friendly tool for designing RNA sequences that fold into multiple target…

A user-friendly tool for designing RNA sequences that fold into multiple target structures. RNAdesign combines a graph-coloring based approach with a sampling method that allows you for the given…

Desktop app
Synthetic Biological… Deprecated Synthetic Biological software based on Google Wave

SynBioWave Synthetic Biological software based on Google Wave

A Google Wave implementation for molecular biologists. SynBioWave aims to unite…

A Google Wave implementation for molecular biologists. SynBioWave aims to unite the stunning possibilities regarding a cooperative workflow of a web application with the comprehensive assortment of…

Web app
RNAinverse RNAinverse

RNAinverse

Allows you to design RNA sequences for any desired target secondary structure.…

Allows you to design RNA sequences for any desired target secondary structure. RNAinverse searches for sequences folding into a predefined structure.

Web app
EternaBot EternaBot

EternaBot

A secondary structure algorithm created by players of Eterna project. Eterna…

A secondary structure algorithm created by players of Eterna project. Eterna players have designed and experimentally tested over 700 sequences. Based the experimental results, they have proposed a…

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