Basic usage

Some of VARNA's main features are demonstrated here, along with the code required to produce them. Have fun!

Hello RNA World!
Hello RNA World!
Sequence Structure Title

This first examples illustrates the most basic usage of the Applet, which is to display a structure/sequence, along with a title... [More]

Uses: sequenceDBN structureDBN title
Round we go...
Round we go...
Algorithm Layout

Using a circular layout, specified by assigning a circular value to the algorithm parameter... [More]

Uses: algorithm sequenceDBN structureDBN title
Pitch black
Pitch black
Coloring options

This third example illustrates how one may fully customize the rendering for a given RNA layout... [More]

Uses: background baseOutline baseInner baseName sequenceDBN structureDBN titleColor title
Funky !
Funky !
Rotating model Creative coloring

Features a very creative usage of color redefinitions. Additionally, a rotation parameter is defined to orient the drawing correctly... [More]

Uses: background baseOutline baseInner baseName bp sequenceDBN structureDBN rotation titleColor title
Multiple panels
Multiple panels
Multiple Panels Sizing Title

This code assigns different colors to each panel, while assigning a common sequence/secondary structure and title to every panel. Notice the usage of titleSize to adapt the title width to that of the panel... [More]

Uses: background columns sequenceDBN structureDBN rotation rows titleSize title
Algorithms
Algorithms
Layout Algorithms

This examples demonstrates the usage of our four different types of representations (layout algorithms) on a single RNA... [More]

Uses: algorithm columns sequenceDBN structureDBN rows titleSize title
Base-pairs styles
Base-pairs styles
Styling Non-Canonical Base-Pairs

Various base-pairs representations, available through the bpStyle parameter. Non-canonical base-pairs, which cannot be specified by parenthesis expresions, are added through the auxBPs parameter, using the Leontis-Westhof nomenclature... [More]

Uses: background bpStyle columns sequenceDBN structureDBN rows titleSize title
Load from URL
Load from URL
Remote locations Multiple File Formats

The applet can be configured to fetch the drawn RNA from the internet, by mean of the url parameter. This feature is illustrated in the above example, where four structures are respectively loaded from applet parameters (NW), from the local HTTP server (NE and SW) and from the NDB server (SE)... [More]

Uses: background columns sequenceDBN structureDBN rows titleSize title url
Planarized
Planarized
Pseudoknots Planarization

Upon loading a pseudoknotted secondary structure, a maximal non-crossing subset of base pairs is extracted and drawn using current algorithm. Remaining base-pairs are drawn in a second-pass, but do not change the coordinates inferred during the initial layout... [More]

Uses: algorithm columns flat sequenceDBN structureDBN rows title
Base Styles
Base Styles
Custom coloring Styling Bases

Custom styles can be specified for individual base by defining a set of basic styles (basesStyle parameter), later to be applied (applyBasesStyle parameter) on subsets of bases. Alternatively, individual base styles can be set using the customBases parameter... [More]

Uses: applyBasesStyleXon customBases basesStyleX sequenceDBN structureDBN title titleSize
Color Maps
Color Maps
Color Map

When the colors have a semantic that is related to a numeric value (Conservation, Boltzmann probability...), VARNA offers the possibility to specify these numeric values and automatically maps these values to colors according to a color map... [More]

Uses: columns colorMap colorMapCaption colorMapStyle rotation rows sequenceDBN structureDBN
Adding Labels
Adding Labels
Annotations Automated labelling

Illustrating the different types of textual annotations can be added to a VARNA drawing: Loop, helix, base or static annotations... [More]

Uses: annotations autoTerminalLoops sequenceDBN structureDBN
Higlighting Regions
Higlighting Regions
Region Highlight Sausage Factory

Highlighting regions, ie sequences of contiguous bases, can be useful to draw the reader's attention toward some local remarkable feature... [More]

Uses: auxBPs baseInner flat highlightRegion sequenceDBN structureDBN title titleSize
Glyphs
Glyphs
Symbols Cheminal Probing

Chemical probing results can be displayed with the chemProb parameter using three types of glyphs: An arrow (type=arrow), a thin triangle (type=triangle) or a pin ending with a diamond (type=pin). Additionally, a custom color (color=#XXYYZZ) and an intensity, denoting the strength of the cleavage (e.g. intensity=1.5) can be specified... [More]

Uses: applyBasesStyleXon basesStyleX baseInner baseOutline chemProb sequenceDBN structureDBN title
Comparing RNAs
Comparing RNAs
Alignment Comparison Consensus Structure

Compatible secondary structures may be jointly represented on a single diagram by annotating their consensus structure... [More]

Uses: comparisonMode firstSequence firstStructure secondSequence secondStructure
JS Interactions I
JS Interactions I
JavaScript Browser Integration

VARNA can be used in slave mode, i.e. be controlled by a browser using a set of functions implemented in the dedicated VARNA.js JavaScript library... [More]

Uses:
JS Interactions II
JS Interactions II
JavaScript Browser Integration

Although a VARNA applet cannot easily push information into the browser, a passive looping technique may still be used to let the browser monitor changes occurring within VARNA... [More]

Uses:

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