Pseudoknot detection software tools | RNA structure data analysis
Pseudoknots are functional structure elements, which have been reported in most classes of RNA. A pseudoknot forms when unpaired bases in a loop pair with complementary bases in a single-stranded region outside the loop.
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.
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.
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 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.
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.
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.
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.