Planarized

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Extracting maximal non-crossing subset: The planarized example
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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.

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<applet  code="VARNA.class"
	codebase="bin"
	archive="VARNA.jar"
	<param name="rows"  value="1" />
	<param name="columns" value="2" />
	<param name="sequenceDBN1" value=
	  "GGGGGGAGGAAACCAAGGGGAAAGGGCCCCACCCCCCAAAAAAGGGGGGCCCAACCCCCC" />
	<param name="structureDBN1" value=
	  "((((((.((...))..((((...[[[)))).))))))......((((((]]]..))))))" />
	<param name="algorithm1" value="circular" />
	<param name="algorithm2" value="radiate" />
	<param name="title1" value="Circular repr." />
	<param name="flat2" value="true" />
	<param name="title2" value="Planarization" />
	</applet>

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