BP styles

Recent changes in Java security policy might prevent you from running VARNA.
Check out this page for details and ways to solve the problem.

Various base-pairs representations: The BP styles example
Java Get Powered

This examples demonstrates four styles of representations for base-pairs. Backgrounds of increasing gray levels are used to mark the boundaries of each panel.

Non-canonical base-pairs, which cannot be specified by parenthesis expresions, are added through the auxBPs parameter, using the Leontis-Westhof nomenclature.

Note to Firefox users: Certain versions of Firefox may be confused by self-signed certificates, and silently prevent the applet from running. If the frame above shows up empty, then try reloading the page. 

<applet  code="VARNA.class"
	codebase="bin"
	archive="VARNA.jar"
	width=500" height="300">
	<param name="rows"  value="1" />
	<param name="columns" value="4" />
	<param name="sequenceDBN1"  value="GAGGGGGGGGGGGGGGGGGGGGGUUC" />
	<param name="structureDBN1" value="(((....................)))" />
	<param name="auxBPs1" value="(4,23):edge5=wc,edge3=h,stericity=trans;
		(5,22):edge5=s,edge3=h,stericity=cis;
		(6,21):edge5=s,edge3=s,stericity=trans;
		(7,20):edge5=h,edge3=h,stericity=cis;
		(8,19):edge5=wc,edge3=wc,stericity=trans;
		(9,18):edge5=h,edge3=wc,stericity=cis" />
	<param name="rotation1" value="-20" />
	<param name="bpStyle1" value="none" />
	<param name="titleSize1" value="17" />
	<param name="title1" value="None" />
	<param name="background1" value="#E0E0E0" />
	<param name="bpStyle2" value="simple" />
	<param name="title2" value="Simple" />
	<param name="background2" value="#E8E8E8" />
	<param name="bpStyle3" value="rnaviz" />
	<param name="title3" value="RNAViz" />
	<param name="background3" value="#F0F0F0" />
	<param name="bpStyle4" value="lw" />
	<param name="title4" value="Leontis/Westhof" />
	<param name="background4" value="#FFFFFF" />
</applet>

^ Top

Previous page: Algorithms
Next page: Load from URL