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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…
ERD
Web
Desktop

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…

incaRNAfbinv
Web

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…

RNAiFold
Desktop
Web

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…

synRNASeqNet
Desktop

synRNASeqNet

Implements various estimators of mutual information. synRNASeqNet executes…

Implements various estimators of mutual information. synRNASeqNet executes several estimator as Millow-Madow, Bayesian or the Chao-Shen. It offers wrappers to the k Nearest Neighbour (kNN) and kernel…

RNAblueprint
Desktop

RNAblueprint

Provides a script collection for Benchmarks and Plots from the publication…

Provides a script collection for Benchmarks and Plots from the publication about the software RNAblueprint. RNAblueprint is like a library equipped with a flexible scripting interface where the user…

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ViennaRNA
Desktop
Web

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…

RNA-Redesign
Web

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…

antaRNA
Desktop
Web

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…

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RNA workbench
Server

RNA workbench

Establishes a central, redistributable workbench for scientists and programmers…

Establishes a central, redistributable workbench for scientists and programmers working with RNA-related data. The RNA workbench builds a sustainable community around it. This platform is unique in…

INFO-RNA
Desktop
Web

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…

Mfold
Web

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,…

IncaRNAtion
Desktop

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.

RNAfbinv
Desktop

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…

RNA Designer
Web

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…

NUPACK
Desktop
Web

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…

RNAexinv
Desktop

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…

Frnakenstein
Desktop

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…

RNAdesign
Desktop

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…

rnadev-models
Desktop

rnadev-models

Provides a system to model RNA designs. rnadev-models is a network context…

Provides a system to model RNA designs. rnadev-models is a network context which models important cellular processes such as transcription, translation and degradation as system of ordinary…

RNAsketch
Desktop

RNAsketch

RNAsketch is a library which allows to design RNA molecules. User can design…

RNAsketch is a library which allows to design RNA molecules. User can design multistate design, sRNA mediated translational regulation, multistate Thermoswitch and can also display a dependency graph.

MODENA
Desktop

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…

RNAinverse
Web

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.

RNA-ensign
Desktop

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…

SynBioWave
Desktop

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…

ARDesigner
Web

ARDesigner Allosteric RNA Designer

Allows allosteric RNA design and incorporates mutational robustness in the…

Allows allosteric RNA design and incorporates mutational robustness in the design process. ARDesigner provides a simple means for researchers to design allosteric RNAs with specific properties. It…

EternaBot
Web

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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