VARNA: Visualization Applet for RNA

Visualizing chemical probing results: The Chemical probing example

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. Finally, the glyph can be displayed inward (dir=in) or outward (dir=out, default), in a poor person's attempt to summarize the impact of several reagents on a single drawing.

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<applet  code="VARNA.class"
	codebase="bin"
	archive="VARNA.jar">
	<param name="basesStyle1" value="fill=#F0F0F0,outline=#D0D0D0" />
	<param name="applyBasesStyle1on"  value="6,17,18" />
	<param name="baseInner"  value="#FFFFFF" />
	<param name="baseOutline"  value="#D0D0D0" />
	<param name="chemProb"  value="11-12:color=#00FF00,dir=out;
		12-13:color=#0000FF,glyph=triangle,dir=in;
		12-13:color=#000000,glyph=pin;
		13-14:color=#0000FF,intensity=0.5,glyph=arrow;
		14-15:intensity=1.5,glyph=triangle" />
	<param name="sequenceDBN"  value="UCGAUCGCAUCGACUACGA" />
	<param name="structureDBN" value="((((((.......))))))" />
	<param name="title" value="Chemical probing" />
	</applet>