Predicts regions with high likelihood of temperature-induced structural changes. RNAtips is a web server which can be used to analyze the location of temperature-induced changes in the secondary structure of RNA and to compare such changes between two sequences of the same length. The software can be applied to a broad spectrum of research topics such as drug development, molecular diagnostic and disease prognosis, evolutionary mechanisms, ecology, investigation of climate change effects.
Calculates statistical values of secondary structures. STOAT is a web application which calculates four statistical values from the secondary structure of folded RNA strings: the Shannon entropy, the Forbenius norm, the Base-pairing propensity and the mean stem length. The secondary structure of the various input sequences are obtained by interactions with the RNAfold program from the Vienna package. The software also translates sequences from FASTA to DCSE format.
Counts the number of unpaired, paired and bulged nucleotides in folded RNA sequences. MARTEN is a web application which codes geometrical features in paired and unpaired regions of the molecules as linearly ordered multistate characters and produces an output for analysis with standard phylogenetic software. The software also translates the secondary structure of folded RNA sequences from the DCSE alignment format to the bracket notation.
Rearranges sequences using a permutation procedure. OMROKGEN is a web application which randomly changes the positions of the nucleotides in a DNA sequence. The software consists of three shuffles, each swapping nucleotides sequentially at all sites with a randomly chosen site elsewhere in the sequence. The number of the various nucleotide types in the generated sequences do not vary from the original sequence and the user can specify the number of sequences to be generated.
Automates the task of coding information in the secondary structure of folded RNA sequences. NOBAI is a web server which consists of four separate modules, MARTEN, STOAT, STRINGGEN and OMROKGEN. The software codes topological and thermodynamic information related to the secondary structure of RNA molecules as multi-state phylogenetic characters, builds character matrices directly and provides sequence randomization options.
Generates all possible combinations of the nucleotides in a DNA sequence. STRINGGEN is a web application which reads a nucleotide sequence and applies a loop to select all possible sequences of that same length and base composition. The number of the various nucleotide types in the generated sequences does not vary from the original sequence. Because of computational limitations, the maximum sequence length is 15 nucleotides.
Implements an algorithm to cluster a set of structured RNAs taking their respective structural conservation into account. For a set of multiple structural alignments of RNA sequences, each containing a paralog sequence included in a structural alignment of its orthologs, RNAscClust computes minimum free-energy structures for each sequence using conserved base pairs as prior information for the folding. The paralogs are then clustered using a graph kernel-based strategy, which identifies common structural features. The clustering accuracy clearly benefits from an increasing degree of compensatory base pair changes in the alignments.
Serves for designing and analyzing structured pools for in vitro selection. RAGPOOLS is an online application assisting in: (1) design of structured RNA pools with target motif distribution; (2) analysis of structural distributions of RNA pools; and (3) research of novel RNAs via combined experimental and theoretical pool design. It is composed of two different tools, RNA Pool Designer and RNA Pool Analyzer.
Offers tools for the visualization of RNA family models, also known as covariance models (CMs) and Hidden Markov Models (HMMs). CMV offers four different visualization tools: (1) HMMV, for visualizing HMMs; (2) HMMCV, for seeing HMM comparisons; (3) CMV, for displaying RNA family models; and (4) CMCV, for studying RNA family comparisons. This tool is available both as a web application and as a standalone software.
Predicts long non-coding RNA (lncRNA) subcellular localization. lncLocator is an ensemble predictor that combines four learning machines using a stacked ensemble strategy. The learning machines are random forest with features extracted by deep neural networks (RFA), support vector machine with features extracted by deep neural networks (SVMA), random forest with raw kmer features (RFR) and support vector machine with raw k-mer features (SVMR), respectively. The software consists of three major steps: (1) feature representation, (2) prediction engine construction, and (3) stacked ensemble.
Permits users to measure the robustness of RNA structures. RNA SC Index is a scoring method that can evaluate the degree of self-containment of an RNA molecule by encapsulating the severity of structure change over a varied number of contexts.
Assists users in inferring and analyzing metal ion effects for nucleic acids. MCTBI provides an interface that allows users to detect ion binding sites, ion-mediated electrostatic free energy of the system or ions binding fraction or the most probable bound ion distribution from a given temperature and ion concentrations coupled to a RNA structure. Users can retrieve their submission by email or by a checking panel.
A method for the automated assignment of RNA imino resonances with synchronized verification and correction of predicted secondary structure. RNA-PAIRS represents an advance in modeling the assignment paradigm because it seeds the probabilistic network for assignment with experimental NMR data, and predicted RNA secondary structure, simultaneously and from the start. Subsequently, RNA-PAIRS sets in motion a dynamic network that reverberates between predictions and experimental evidence in order to reconcile and rectify resonance assignments and secondary structure information.
Predicts RNA chemical shifts. LARMORD allows chemical shifts to be easily incorporated into molecular simulations of RNA. It was created by compiling a training set consisting of RNAs for which nuclear magnetic resonance (NMR) structures were available via the Protein Data Bank (PDB) and chemical shifts. The tool uses a polynomial expansion of distances between the nucleus of interest and all heavy atoms with a biomolecule to proceed.
Generates Markov models of k-vertex adjacency matrices representing the RNA. StreAM-Tg is based on a coarse-grained representation of RNA molecular dynamics (MD) simulations. It permits to gain insights into RNA dynamics. The tool combines every adjacency-based transition matrix, one nucleotide participates in, into a global model. It permits to make efficient analysis of large MD trajectories.
Assists users in calculating the block-interchange distance of a permutation. SBBI is a polynomial-time algorithm. This method was implemented in 2 versions: (i) an interactive application that has a quadratic runtime where user only needs to enter a permutation or create a random permutation of length, and (ii) a desktop version that runs in time O(n log n) instead of O(n2).
Investigates chemical mapping data derived from next generation sequencing (NGS) experiments. MAPseeker proposes a standalone software which is able to numbers nucleotides’ reactivities into each RNA in each condition. The application enables the enhancement of ssDNA adapters’ ligations efficiency as well as to avoid polymerase chain reactions (PCR) phases for purposes of diminishing biases.
Visualizes protein structures DNA/RNA sequences into a virtual reality (VR) environment. BioVR proposes a platform usable through Oculus Rift intending to facilitate an interactive browsing of genomic variants. The application aims to assists users in highlighting sequence-structure relationship of important residues of a protein. It was tested on a representation of the Gria2 gene of Rattus norvegicus.
Allows users to visualize RNA family models, also known as covariance models (CM). CMV is a web application that assists users to obtain alignments in stockholm format. To perform, users have to download on the platform two different files containing: (1) covariance models (CM); or (2) structural alignments.
Categorizes the RNA backbone geometry from dihedral-angle input for a specific RNA structure. Suitename is a C program that supports the RNA Ontology Consortium (ROC) consensus RNA backbone nomenclature and conformer-list development. This application is built into MolProbity. It produces entries in the multi-criterion chart for an RNA model as well as a suite string file.
Computes joint and individual partition functions for two RNA sequences. piRNA is an efficient algorithm to calculate a partition function of two interacting nucleic acid strands. This method considers almost all physically possible secondary structures that do not contain pseudoknots, crossing interactions and ‘zigzag’s. It also estimates equilibrium concentrations of single and double joint species, ensemble energy, and melting temperatures.
Examines the evolution of robustness based on biologically important landscapes induced by RNA folding. EvoRSR uses different mechanisms for ensuring robustness such as thermodynamic stability at the RNA and protein level to behavior at the organismal level. The method of this software can be applied to the evolution of robustness in protein structures with more accurate prediction algorithms.
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