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. Source text: Sperschneider and Datta, 2010.
Allows extraction of an RNA secondary structure from atom coordinate data collected and presentation of this structure it in both textual and graphical form. RNApdbee is a web server that provides two usage scenarios: the (1) 3D scenario (the basic one) to derive the secondary structure topology of RNA from the pdb data and the (2) 2D scenario to convert between the CT, BPSEQ and extended dot-bracket notations.
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 line segments. PseudoViewer3 is about 10 times faster than PseudoViewer2.
Allows users to simulate nucleic acid folding and hybridization for single-stranded sequences. UNAFold is a program that aims to determine folding for single-stranded RNA or DNA through combination of stochastic sampling, partition function calculations and free energy minimization. To realize melting simulations, it calculates the integrality of melting profile and not only temperatures. Images concerning hybridizations or secondary structure can be compute thanks to common formats.
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 regions. RNA-Decoder employs a stochastic context-free grammar together with a set of carefully devised phylogenetic substitution-models, which can disentangle and evaluate the different kinds of overlapping evolutionary constraints which arise. On known secondary structures, RNA-Decoder shows a sensitivity similar to the programs Mfold, Pfold and RNAalifold. When scanning the entire genomes of Hepatitis C virus (HCV) and polio virus for structure elements, RNA-Decoder's results indicate a markedly higher specificity than Mfold, Pfold and RNAalifold.
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 direct connections. Edge weights correspond to saddle energy of the connection. Framework uses many heuristics, so resulting graph is not exact every time. Exact enumeration techniques are unfortunately limited to small RNA molecules.
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 pseudoknots and intramolecular kissing hairpins are constructed and their presence in the sequence is verified. The detected pseudoknots can then be further analysed using bioinformatics or laboratory techniques.
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 tautomeric or protonation state. It detects higher-order coplanar base associations, termed multiplets. DSSR finds arrays of stacked pairs, classifies them by base-pair identity and backbone connectivity, and distinguishes a stem of covalently connected canonical pairs from a helix of stacked pairs of arbitrary type/linkage. DSSR identifies coaxial stacking of multiple stems within a single helix and lists isolated canonical pairs that lie outside of a stem. The program characterizes ‘closed’ loops of various types (hairpin, bulge, internal, and junction loops) and pseudoknots of arbitrary complexity. Notably, DSSR employs isolated pairs and the ends of stems, whether pseudoknotted or not, to define junction loops.
An extension of PseudoBase for easy searching, formatting and visualization of pseudoknots. PseudoBase++ maps the PseudoBase dataset into a searchable relational database including additional functionalities such as pseudoknot type. PseudoBase++ links each pseudoknot in PseudoBase to the GenBank record of the corresponding nucleotide sequence and allows scientists to automatically visualize RNA secondary structures with PseudoViewer. It also includes the capabilities of fine-grained reference searching and collecting new pseudoknot information.
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 conformations. The search algorithm has no restriction in terms of pseudoknot complexity. Another aspect is that at each step during the simulated folding process, the steric feasibility of the predicted structures is checked for steric feasibility using a highly coarse-grained 3D representation.
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 minimum free energy structure regardless of pseudoknot topology. This unique proficiency is obtained at the expense of the maximum length of sequences that can be treated, but comparison with state-of-the-art algorithms shows that TT2NE significantly improves the quality of predictions.
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 1000 bases and performs an advanced stochastic search of their minimum free energy structure allowing for non-trivial pseudoknot topologies. Specifically, McGenus uses a Monte Carlo algorithm with replica exchange for minimizing a general scoring function which includes not only free energy contributions for pair stacking, loop penalties, etc. but also a phenomenological penalty for the genus of the pairing graph.
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 with pseudoknots and RactIP for predicting RNA-RNA interactions with kissing hairpins. Both servers can run much faster than existing services with the same purpose on large data sets as well as being at least comparable in prediction accuracy.
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 substructures and approximates a base-pairing probability distribution that considers pseudoknots, leading to the capability of modeling a wide class of pseudoknots and running quite fast.
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 pseudoknot from pknotsRG. The new class is canonical simple recursive kissing hairpins.
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 a hand-curated test set of RNA structures with experimental support. It uses RNAfold and RNAeval from the Vienna RNA Package for producing the probability dot plot and for free energy evaluation of secondary structure elements.
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 and benefits from comparative sequence analysis.
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 idea to just draw their arcs on a more complex topological surface in order to resolve crossings. Random matrix theory integrated facilitates the classification and expansion of pseudoknotted structures in terms of topological genus.
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 structures, using a free energy minimization algorithm for pseudoknot free secondary structures to identify promising candidate stems.
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 helpful in increasing accuracy. Note also that if a pseudoknot-containing structure is predicted, it will be displayed as a circular structure. If the predicted structure does not contain pseudoknots, it will be displayed as a radial structure.
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 approach to perform a screening of the primary sequence.
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 conduct genome-scale pseudoknot-containing ncRNA search effectively and efficiently. It provides a complementary pseudoknot search tool to Infernal.
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 junction prediction, (iii) graphs are sampled by Monte Carlo, (iv) candidate graphs are assessed and compared with reference graphs, and (v) all atom models are constructed by graph partitioning, fragment search, and assembly of corresponding all atom.
Forecasts nucleic acid complexes that possibly include pseudoknots. HyperFold is a method which highlights pairs of secondary structures with different strand connectivity and similar-placed helices except one. The application is based on a search algorithm coupled to methods enabling the determination of entropic contributions and kinetic accessibility. Besides, it can determine the base pairing of RNA/RNA, DNA/DNA, and RNA/DNA hybrid interactions.
Permits to calculate the entropy of RNA structure. RNA-FE-Landscape is a method that treats both pseudo-knotted and non-pseudo-knotted RNA structures equivalently. This algorithm permits users to return all possible secondary structures resulting from the primary sequence. It also offers the probability of folding into a pseudo-knotted structure for each sequence. It can be easily generalized to probe multiple interacting strands.
Provides a method for performing RNA secondary structures prediction. P-DCFold is an algorithm, based on the comparative approach that performs a recursive search on helices and ranks them from the most to the less significant. It can be used to detect non-interleaved helices and was developed especially for predicting the presence of pseudoknots.
Provides structure prediction for a comprehensive class of biologically relevant pseudoknots. Knotty is a minimum free energy (MFE) method that offers a unique feature set that enables novel applications for computational pseudoknot structure prediction. It aims to develop large scale biologically-relevant applications of pseudoknot structure prediction covering all important pseudoknot classes.
Performs secondary RNA complex predictions. RcPred is a software proposing an approach based on a combination of tabu and local searches, built around a constrained maximum weight clique graph problem (MCP). The application does not depend of any RNA ordering and is able to consider pseudoknots, crossing interactions, zig-zags as well as non-Watson-Crick base pairs with known energy.
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 tool is available as source code, binary executable, online tool or as Web Service. The latter alternative allows for an easy integration into bio-informatics pipelines.
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 building blocks.
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 probabilistic criteria.
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 tool for shape prediction. By combining the predicted shapes and the multiple structural alignment strategy, KnotStructure demonstrates higher accuracy in pseudoknot structure prediction.
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 well-known algorithms, it has good running efficiency and shows better performance in terms of prediction sensitivity, specificity and positive control on pseudoknotted sequences.
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 approach calculates the optimally lowest stacking energy between two partner sequences. Combined with the Mfold, PLMM_DPSS can also be used in predicting complicated pseudoknots.
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