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 RNA-based biotechnology and synthetic biology, reliable RNA sequence design becomes a crucial step to generate novel biochemical components.
Gathers an assortment of methods for RNA secondary structure analyses. ViennaRNA provides a unified interface to a set of command-line programs dealing with: (i) noncoding RNA detection, (ii) three different algorithms for structure prediction, (iii) RNA folding kinetics, (iv) sequence design considering RNA-RNA hybridizations, and (v) utilities that mainly assist in processing input- and output data and more.
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, single strand frequency plots and 'energy dot plots', are available for the folding of single sequences.
A web tool crafted to simplify the process of CRISPR guide selection in an input DNA sequence by (i) discovering possible offtargets genome-wide, (ii) highlighting guides with high target specificity, and (iii) flagging guides with numerous or genic offtargets in target genomes. The CRISPR design tool allows users to enter a 23-1000bp DNA sequence of interest and will find all SpCas9 target sites within the input sequence. The result will contain a rank ordered list of target sites based on predicted specificity.
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 complexes of nucleic acid strands intended to adopt a target secondary structure at equilibrium.
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 functions, a structure stability score and structure similarity score. MODENA can simultaneously design multiple different RNA sequences at 1 run, whose lowest free energies range from a very stable value to a higher value near those of natural counterparts.
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 defunct COMET language to C++. The new code properly extends the capabilities of its predecessor by providing a user-friendly pipeline to design synthetic constructs having the functionality of given Rfam families. In addition, the new software supports amino acid constraints, even for proteins translated in different reading frames from overlapping coding sequences; moreover, structure compatibility/incompatibility constraints have been expanded. With these features, RNAiFold 2.0 allows the user to design single RNA molecules as well as hybridization complexes of two RNA molecules.