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Secondary structure visualization software tools | RNA data analysis

Visually examining RNA structures can greatly aid in understanding their potential functional roles and in evaluating the performance of structure prediction algorithms. As many functional roles of RNA structures can already be studied given the…
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RiboVision
Web
Desktop

RiboVision

Analyzes, retrieves, filters, and displays diverse information, simultaneously…

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…

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Structurexplor
Web

Structurexplor

Furnishes a web-based tool platform to enable the exploration process for RNA…

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…

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forna
Desktop
Web

forna force-directed RNA

A web-based tool for displaying RNA secondary structure which allows users to…

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,…

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RNAmap2D
Desktop

RNAmap2D

Calculates and visualizes nucleic acid contact and distance maps. RNAmap2D…

Calculates and visualizes nucleic acid contact and distance maps. RNAmap2D intends to improve analyzes of RNA structures which focus on type and location of short-range interactions, without taking…

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JNSViewer
Web

JNSViewer JavaScript-based Nucleotide Sequence secondary structure Viewer

Offers a web interface that can present precise connection among nucleotide…

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…

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VARNA
Desktop

VARNA Visualization Applet for RNA

A Java lightweight Applet dedicated to drawing the secondary structure of 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…

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RnaViz
Desktop

RnaViz

A user-friendly, portable, windows-type program for producing…

A user-friendly, portable, windows-type program for producing publication-quality secondary structure drawings of RNA molecules. RnaViz 2 supports CT, DCSE, and RNAML input formats and improves on…

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RNA Movies
Desktop

RNA Movies

A system for the visualization of RNA secondary structure spaces. 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,…

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PseudoViewer
Desktop
Web

PseudoViewer

An XML web service and web application program for visualizing RNA secondary…

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…

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RNALogo
Web

RNALogo

Presents a graphical representation of the patterns in an aligned RNA sequences…

Presents a graphical representation of the patterns in an aligned RNA sequences with a consensus structure. Several significant features, including sequence conservation, structural conservation, and…

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RNAMLview
Desktop

RNAMLview

A visualization tool that displays/edits 2-dimensional diagrams of RNA/DNA…

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…

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R-CHIE
Desktop
Web

R-CHIE

Allows you to make arc diagrams of RNA secondary structures, allowing for easy…

Allows you to make arc diagrams of RNA secondary structures, allowing for easy comparison and overlap of two structures, rank and display basepairs in colour and to also visualize corresponding…

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jViz.Rna
Desktop

jViz.Rna

A multi-platform visualization tool capable of displaying and comparing RNA…

A multi-platform visualization tool capable of displaying and comparing RNA secondary structures encoded in a number of file formats. Structures can be shown using six different visualization modes…

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RNA-DV
Web
Desktop

RNA-DV

Allows to visualize and design RNA secondary structures. RNA-DV provides an…

Allows to visualize and design RNA secondary structures. RNA-DV provides an interactive visualization interface with supports in structural editing capability. The software incorporates four…

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RNAfdl
Desktop

RNAfdl RNA force directed layout

Allows manual editing and several drawing styles, as well as a fully automated…

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…

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RILogo
Desktop
Web

RILogo

A program to visualize inter- and intramolecular base pairing between two RNA…

A program to visualize inter- and intramolecular base pairing between two RNA molecules. The input for RILogo is a pair of structure-annotated sequences or alignments. In the latter case, RILogo…

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4SALE
Desktop

4SALE

Designs to handle sequence and secondary structure information of RNAs…

Designs to handle sequence and secondary structure information of RNAs synchronously. By including a complete new method of simultaneous visualization and editing RNA sequences and secondary…

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RNA2DMap
Web

RNA2DMap

Allows to visualize multiple types of information on an RNA secondary…

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…

MultiRNAFold
Desktop

MultiRNAFold

Contains software for secondary structure prediction of one, two, or many…

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.…

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RNAbows
Web

RNAbows

A visualization tool for RNA base pair probabilities. RNAbows represent base…

A visualization tool for RNA base pair probabilities. RNAbows represent base pair probabilities with line thickness and shading, yielding intuitive diagrams. RNAbows aid in disentangling incompatible…

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R2R
Desktop

R2R

Makes it possible to obtain high-quality drawings of the consensus sequence and…

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…

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LoopDLoop
Desktop

LoopDLoop

Draws RNA secondary structures in molecular biology. LoopDLoop provides…

Draws RNA secondary structures in molecular biology. LoopDLoop provides graphical views of the sequence's secondary molecular structure and options which allow to modify, adorn and edit the…

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XRNA
Desktop
Web

XRNA

A Java based suite of tools for the creation, annotation and display of RNA…

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…

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