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RNA Movies
A system for the visualization of RNA secondary structure spaces. RNA Movies can be used to visualize structural rearrangement processes of RNA, such as folding pathways and conformational switches, or to browse lists of alternative structure candidates. RNA Movies supports the DCSE and RNAStructML input formats besides its own RNM format. Pseudoknots and 'entangled helices' can be superimposed on the RNA secondary structure layout. Publication quality output is provided through the Scalable Vector Graphics output format understood by most current drawing programs.
A visualization tool that displays/edits 2-dimensional diagrams of RNA/DNA secondary structures with tertiary interactions created by RNAView. RNAMLview generates standard molecular representations (e.g. tRNA cloverleaf structures) or any structural representation desired by the user by rearranging various parts (e.g helices and single strands) of the RNAView 2D diagrams. RNA motifs are rapidly identified and classified with the base pair annotation and the 2D graphic display.
VARNA / Visualization Applet for RNA
A Java lightweight Applet dedicated to drawing the secondary structure of RNA. VARNA implements four drawing algorithms, supports input/output using the classic formats dbn, ct, bpseq and RNAML and exports the drawing as five picture formats, either pixel-based (JPEG, PNG) or vector-based (SVG, EPS and XFIG). It also allows manual modification and structural annotation of the resulting drawing using either an interactive point and click approach, within a web server or through command-line arguments.
forna / force-directed RNA
A web-based tool for displaying RNA secondary structure which allows users to easily convert sequences and secondary structures to clean, concise and customizable visualizations. forna supports, among other features, the simultaneous visualization of multiple structures, the display of pseudoknotted structures, the interactive editing of the displayed structures, and the automatic generation of secondary structure diagrams from PDB files. It requires no software installation apart from a modern web browser.
RNAfdl / RNA force directed layout
Allows manual editing and several drawing styles, as well as a fully automated conjugate gradients minimization approach to draw more complex structures without user interaction. RNAfdl is a highly flexible tool for drawing RNA secondary structures. Secondary structures can be visualized as classical secondary structure plot, circle plot, linear plot or mountain plot. It is capable of producing intersection-free diagrams for ribosome-sized structures, has a graphical user interface (GUI) for adjustments and produces output in common formats.
Furnishes a web-based tool platform to enable the exploration process for RNA secondary structures. Structurexplor generates clusters and structure hierarchies and provides information about the most representative and unusual structural shapes of RNA by the identification of representative and unusual structures of clusters. Thanks to an interactive visualization, users can explore structural features of secondary structures from both linear and circular RNA, and to take pseudoknots and G-quadruplexes into account.
Contains software for secondary structure prediction of one, two, or many interacting RNA or DNA molecules. MultiRNAFold is composed of three pieces of software: SimFold, PairFold and MultiFold. SimFold predicts the minimum free energy (MFE) secondary structure of a given input RNA or DNA sequence. PairFold predicts the MFE secondary structure of two interacting RNA or DNA molecules, and suboptimal structures. MultiFold predicts the MFE secondary structure of three or more RNA/DNA input sequences.
Analyzes, retrieves, filters, and displays diverse information, simultaneously on 1D, 2D and 3D structure from ribosomes of six different species. RiboVision is a web-based portal which allows to map and display new and preloaded data, swapp data between species, and generates images on any level of structure. The software can maintain and display multiple layers of information, with controllable transparency. It also allows users to import data and map it directly onto all levels of structure.
PRI-Modeler / protein–RNA interaction modeler
Recognizes the secondary and tertiary structures of RNA. PRI-Modeler analyzes the hydrogen bond and van der Waals interactions between protein and RNA from the three-dimensional atomic coordinates of protein-RNA complexes in the protein data bank. It identifies base pairs and classifies base pairs into 28 types to extract secondary and tertiary structures. It can analyze multiple PDB files at once and provides the analysis report on protein-RNA interactions in all the PDB files analyzed.
JNSViewer / JavaScript-based Nucleotide Sequence secondary structure Viewer
Offers a web interface that can present precise connection among nucleotide sequences, pairing and folding information, biological annotations, and secondary structure graphs. JNSViewer is a web service for DNA/RNA secondary structure visualization. This web app is bundled with several popular RNA or DNA prediction software for comparative secondary structure predictions, including RNAfold, RNAshapes, RNAsubopt, RNAstructure and Mfold. Its permits users to customize RNA structure predictions with different programs and settings.
repRNA / representations of RNA sequences
A web application for generating various modes of RNA sequences. Compared with the existing methods, repRNA is much more comprehensive, flexible and powerful, as reflected by the following facts: (1) it can generate 11 different modes of feature vectors for users to choose according to their investigation purposes; (2) it allows users to select the features from 22 built-in physicochemical properties and even those defined by users' own; (3) the resultant feature vectors and the secondary structures of the corresponding RNA sequences can be visualized.
Makes it possible to obtain high-quality drawings of the consensus sequence and structural models of many diverse RNA structures with a more practical amount of effort. R2R is a computer program that facilitates the generation of aesthetic and readable drawings of RNA consensus diagrams in a fraction of the time required with general-purpose drawing programs. It can be used to create consensus sequence and secondary structure models for novel RNA structures or to revise models when new representatives for known RNA classes become available.
Allows to visualize multiple types of information on an RNA secondary structure. RNA2DMap is a structural interface which enables to select, customize and display multiple-dimensions of information about RNA structure, to visually identify patterns and relationships. The software also highlights base pairing, conformation, motif and conservation values, and shows distance values in 3D space. It can help the comparative analysis and understanding of RNAs that cannot be readily obtained with other output from computer programs.
A Java based suite of tools for the creation, annotation and display of RNA secondary structure diagrams. XRNA provides editing tools for easy modification of publication quality secondary diagrams that can be either drawn manually, or through automatic generation. Other features include grouping, numbering and structure annotation. XRNA secondary structures may be saved in a native format, or exported as postscript for printing and further manipulation in programs such as Adobe Illustrator.
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