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Pseudoknot detection software tools | RNA structure data analysis

Pseudoknots are functional structure elements, which have been reported in most classes of RNA (Brierley et al., 2007). A pseudoknot forms when unpaired bases in a loop pair with complementary bases in a single-stranded region outside the loop.…
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NanoFolder
Web

NanoFolder

A method for the prediction of the base pairing of potentially pseudoknotted…

A method for the prediction of the base pairing of potentially pseudoknotted multistrand RNA nanostructures.

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DSSR
Desktop

DSSR Dissecting the Spatial Structure of RNA

An integrated and automated tool for analyzing and annotating RNA tertiary…

An integrated and automated tool for analyzing and annotating RNA tertiary structures. DSSR identifies canonical and noncanonical base pairs, including those with modified nucleotides, in any…

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pKiss
Desktop
Web

pKiss

A tool for folding RNA secondary structures, including two limited classes of…

A tool for folding RNA secondary structures, including two limited classes of pseudoknots. As pKiss is the successor of pknotsRG, the first pseudoknot class is the canonical simple recursive…

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RNApdbee
Web

RNApdbee

Allows to extract RNA secondary structure from the pdb file, and presents it in…

Allows to extract RNA secondary structure from the pdb file, and presents it in both textual and graphical form. RNApdbee supports processing of knotted and unknotted structures of large RNAs, also…

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HotKnots
Web

HotKnots

A heuristic algorithm for the prediction of RNA secondary structures including…

A heuristic algorithm for the prediction of RNA secondary structures including pseudoknots. Based on the simple idea of iteratively forming stable stems, HotKnots explores many alternative secondary…

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BHG
Desktop

BHG Basin Hopping Graph

Aims to construct a landscape abstraction, or a basin hopping graph (BHG), of…

Aims to construct a landscape abstraction, or a basin hopping graph (BHG), of RNA secondary structure landscape of a chosen sequence. Nodes of BHG represent local minima basins and edges available…

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IPknot
Desktop
Web

IPknot

Predicts RNA secondary structures with pseudoknots based on maximizing expected…

Predicts RNA secondary structures with pseudoknots based on maximizing expected accuracy of a predicted structure. IPknot decomposes a pseudoknotted structure into a set of pseudoknot-free…

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ProbKnot
Web

ProbKnot

Takes a sequence file of nucleic acids, either DNA or RNA, and predicts the…

Takes a sequence file of nucleic acids, either DNA or RNA, and predicts the presence of pseudoknots in its folded configuration. Note that increasing the number of calculation iterations may be…

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DotKnot
Desktop
Web

DotKnot

A heuristic method for pseudoknot prediction in a given RNA sequence. DotKnot…

A heuristic method for pseudoknot prediction in a given RNA sequence. DotKnot extracts stem regions from the secondary structure probability dot plot calculated by RNAfold. Recursive H-type…

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Sampler
Desktop

Sampler

A Boltzmann sampler for peudoknotted structures. Compared to existing tools…

A Boltzmann sampler for peudoknotted structures. Compared to existing tools which were designed with the dynamic programming paradigm, Sampler allows to have topological structures from the intuitive…

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PseudoBase
Dataset

PseudoBase

A database containing structural, functional and sequence data related to RNA…

A database containing structural, functional and sequence data related to RNA pseudo-knots. For each pseudoknot, thirteen items are stored, for example the relevant sequence, the stem positions of…

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McQFold
Desktop

McQFold

A program for MCMC-sampling secondary structures with pseudoknots for a given…

A program for MCMC-sampling secondary structures with pseudoknots for a given RNA sequence.

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PseudoViewer
Desktop
Web

PseudoViewer

An XML web service and web application program for visualizing RNA secondary…

An XML web service and web application program for visualizing RNA secondary structures with pseudoknots. PseudoViewer3 generates a compact drawing by representing a loop as a path of circles and…

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pknotsRG
Desktop
Web

pknotsRG

A software tool for single sequence RNA secondary structure prediction…

A software tool for single sequence RNA secondary structure prediction including pseudoknots. pknotsRG employs the newest Turner energy rules for finding the structure of minimal free energy. The…

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Rtips
Desktop
Web

Rtips

A web-based tool for fast and accurate prediction of RNA 2D complex structures.…

A web-based tool for fast and accurate prediction of RNA 2D complex structures. Rtips comprises two computational tools based on integer programming, IPknot for predicting RNA secondary structures…

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McGenus
Web

McGenus

An algorithm to predict RNA secondary structures with pseudoknots. The method…

An algorithm to predict RNA secondary structures with pseudoknots. The method is based on a classification of RNA structures according to their topological genus. McGenus can treat sequences of up to…

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PseudoBase++
Web

PseudoBase++

An extension of PseudoBase for easy searching, formatting and visualization of…

An extension of PseudoBase for easy searching, formatting and visualization of pseudoknots. PseudoBase++ maps the PseudoBase dataset into a searchable relational database including additional…

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TT2NE
Web

TT2NE

An algorithm to predict RNA secondary structures with pseudoknots. The method…

An algorithm to predict RNA secondary structures with pseudoknots. The method is based on a classification of RNA structures according to their topological genus. TT2NE is guaranteed to find the…

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URSDB
Dataset

URSDB Universe of RNA Structures DataBase

A database that stores information obtained from all RNA-containing PDB…

A database that stores information obtained from all RNA-containing PDB entries. URSDB consists of 51 tables containing indexed data on various elements of the RNA structures. The database provides a…

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RAGTOP
Desktop

RAGTOP RNA-As-Graph-TOPologies

Predicts global 3D topologies compatible with a given RNA 2D structure. RAGTOP…

Predicts global 3D topologies compatible with a given RNA 2D structure. RAGTOP is a hierarchical sampling approach: (i) a 2D tree topology is annotated, (ii) an initial planar graph is constructed by…

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DotKnot-PW
Desktop

DotKnot-PW

A comparative pseudoknot prediction method based on structural comparison of…

A comparative pseudoknot prediction method based on structural comparison of secondary structure elements and H-type pseudoknot candidates. DotKnot-PW outperforms other methods from the literature on…

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PhyloQFold
Desktop

PhyloQFold

A program for Bayesian sampling of evolutionarily conserved RNA secondary…

A program for Bayesian sampling of evolutionarily conserved RNA secondary structures with pseudoknots. PhyloQFold is able to accept a multiple sequence alignment and a phylogenetic tree as an input…

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gfold
Desktop

gfold

Predicts RNA structures with pseudoknots. The idea behind gfold is to define a…

Predicts RNA structures with pseudoknots. The idea behind gfold is to define a more suitable class of structures that can be generated by nesting and concatenating a small number of elementary…

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KnotSeeker
Desktop
Web

KnotSeeker

A heuristic algorithm for the detection of pseudoknots in RNA sequences as a…

A heuristic algorithm for the detection of pseudoknots in RNA sequences as a preliminary step for structure prediction. KnotSeeker uses a hybrid sequence matching and free energy minimization…

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knotsearch
Desktop

knotsearch

A pseudoknot search tool using multiple simple sub-structures, which are…

A pseudoknot search tool using multiple simple sub-structures, which are derived from knot-free and bifurcation-free structural motifs in the underlying family. This sub-structure based tool can…

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KnotShape/KnotS…
Desktop

KnotShape/KnotStructure

Predict shapes and secondary structures on hundreds of ncRNA data sets with and…

Predict shapes and secondary structures on hundreds of ncRNA data sets with and without psuedoknots. The combination of mass data analysis and SVM-based feature ranking makes KnotShape a promising…

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BiokoP
Web

BiokoP

Predicts pseudoknots from specific motifs of RNA secondary structures. BiokoP…

Predicts pseudoknots from specific motifs of RNA secondary structures. BiokoP combines different models such as thermodynamic or comparative models. It permits the optimization of both energy and…

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UNAFold
Web

UNAFold Unified Nucleic Acid Folding

An integrated collection of programs that simulate folding, hybridization, and…

An integrated collection of programs that simulate folding, hybridization, and melting pathways for one or two single-stranded nucleic acid sequences. Folding (secondary structure) prediction for…

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CyloFold
Web

CyloFold

A computational approach for RNA secondary structure prediction that has no…

A computational approach for RNA secondary structure prediction that has no restriction in terms of pseudoknot complexity, but additionally checks the steric feasibility of the considered…

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RNA-Decoder
Web
Desktop

RNA-Decoder

Takes the known protein-coding context of an RNA-sequence alignment into…

Takes the known protein-coding context of an RNA-sequence alignment into account in order to predict evolutionarily conserved secondary-structure elements, which may span both coding and non-coding…

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FlexStem
Desktop

FlexStem

Predicts RNA secondary structures with pseudoknots. FlexStem is tested on a…

Predicts RNA secondary structures with pseudoknots. FlexStem is tested on a large number of sequences taken from Sprinzl, 5SrRNAs, Pseudobase and other reliable resources. Compared with other…

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PLMM_DPSS
Web

PLMM_DPSS Pseudoknot Local Motif Model and Dynamic Partner Sequence Stacking

Predicts all PLM model pseudoknots within an RNA sequence in a…

Predicts all PLM model pseudoknots within an RNA sequence in a neighboring-region-interference-free fashion. The PLM model is derived from the existing Pseudobase entries. The innovative DPSS…

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