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UNAFold / Unified Nucleic Acid Folding
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.
DSSR / Dissecting the Spatial Structure of RNA
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. 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.
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