Generates a set of 3-D structure models from a syntactic definition of the modeled RNA molecule. MC-Sym is an RNA 3-D structure modeling system. It creates a conformational search space from this input into which conformations are built and validated according to a set of constraints. It includes sequence constitution and nucleotide-nucleotide interaction types.
Predicts RNA secondary structures from sequence. MC-Fold is a part of an RNA-structure-prediction method based on nucleotide cyclic motifs (NCMs). This application is implemented as a pipeline with MC-Sym, an other computer program that predicts all-atoms RNA tertiary structure from sequence and secondary structure. MC-Fold takes into account the in-stem non-canonical base pairs, and suites of, into a unified energetic framework.
Identifies cloverleaf structure for each sequence. MC-Cons computes a program that assigns an RNA secondary structure among sub-optimals for many sequences, such that the assigned secondary structures maximize the resemblance to all others. It assigns to each sequence the structure that maximizes the overall sum of pairwise structural similarities. This online application can also be seen as a filter between multiple-sequences and tertiary structure.
Allows RNA secondary structure prediction and analysis. RNAstructure is designed to make algorithms accessible for a variety of user needs. The software includes methods for predicting bimolecular structure, conserved structures in multiple homologs and siRNA design. Several methods are also available for predicting structures for a single sequence, including maximum expected accuracy, stochastic sampling, exhaustive traceback and pseudoknot prediction.
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.
A RNA secondary structure prediction tool based on the idea of combining small motifs, called nucleotide cyclic motifs (NCMs). The algorithm implemented here has polynomial runtime in O(n^3) and uses a (pseudo-energy) scoring scheme. This program uses the same database as MC-Fold (which has exponential run-time) and aims to be able to produce the same results. The underlying grammar of our implementation is unambiguous and allows the complete evaluation of all structures within an energy band above the ground state, presenting each unique structure just once. Alternatively, the grammar allows partition function calculations.
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.
Analyzes a multiple RNA sequence alignment and quantitates the statistical support for evolutionary conservation of an RNA structure. R-scape is a web application that determines the statistical significance of the observed covariation scores. For a given alignment, it produces many simulated null alignments and calculates an average product corrected (APC) G-test statistic for each alignment column pair.
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.
Detects structured noncoding RNAs in comparative genomics data. RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. It can be used in genome wide screens to detect functional RNA structures, as found in noncoding RNAs (ncRNAs) and cis-acting regulatory elements of messenger RNAs (mRNAs). The algorithm allows to calculate thermodynamic stability scores based on a dinucleotide background model.
Deals with RNA structure probing and post-transcriptional modifications mapping high-throughput data. RNA Framework is a modular toolkit. Its main features are (i) automatic reference transcriptome creation, (ii) automatic reads preprocessing (adapter clipping and trimming) and mapping, (iii) scoring and data normalization and (iv) accurate RNA folding prediction by incorporating structural probing data. It can perform not only RNA Structure analysis, but also analysis of RNA post-transcriptional modifications mapping experiments (such as m1A-seq, m6A-seq, 2OMe-seq, and Pseudo-seq).
Facilitates distributed access to bioinformatics command line programs. JABAWS provides functions for alignments and sequence analyses of up to 1000 sequences with up to 1000 residues. This tool assists users to recognize potential performance issues and aids with web services troubleshooting. It is able to determine amino acid alignment conservation.
Serves for structural alignment of a binary tree and a sequence. PHMMTSs can be applied to aligning RNA secondary structures, i.e. a pairwise alignment to align an unfolded RNA sequence into an RNA sequence of known secondary structure. This tool assists users to identify non-coding RNA regions in an unfolded RNA sequence by aligning it into non-coding RNAs of known secondary structure. Moreover, this tool can be used for calculating structural alignments of RNA sequences.
Takes an alignment of RNA sequences as input and predicts a common structure for all sequences. Pfold is based on the KH-99 algorithm, which was only useful for a limited number of sequences due to its large computation time. This work makes the algorithm practically useful for larger numbers of sequences. The main concerns are treatment of gaps, computational speed and robustness. A new version of this algorithm has been created, called PPfold. PPfold is a parallelized version of Pfold, and can predict the structure of much longer alignments without underflow errors.
Establishes a central, redistributable workbench for scientists and programmers working with RNA-related data. The RNA workbench builds a sustainable community around it. This platform is unique in combining available tools, workflows and training material, as well as providing easy access for experimentalists. It serves as a central hub for programmers, which can easily integrate and deploy their existing or novel tools and workflows.
Allows determination of perturbation energies that minimizes the differences between predicted and observed pairing probabilities. RNApbfold is an online application that requires a sequence in FASTA format or shape reactivities for performing. For a sequence, this tool accepts until 1000nt. Furthermore, users can be notified via e-mail upon completion of the job.