VARNA: Visualization Applet for RNA

Visualizing the consensus of two compatible RNAs: The Comparing RNAs example

Two secondary structures may be jointly represented on a single diagram by annotating their consensus structure. To that purpose, the input structures must be compatible, i.e. any base-pair in the first structure must be compatible with any base-pair in the second structure. In other words, both structures must be captured by a super-secondary structure (aka consensus structure), which contains the base-pairs of both structures (w/o inducing a pseudoknot).

In the resulting diagram, conserved positions are drawn as usual, whereas divergent positions are represented by double nodes, indicating either a mismatch or an indel.

To specify such a visualization mode, one must:

• Set the comparisonMode parameter to true
• Provide two sequences by setting the firstSequence and secondSequence parameters to some string, using the dot '.' character to denote gaps.
• Provide two structures through the firstStructure and secondStructure parameters, using the dot '.' character indifferently to denote gaps and unpaired bases.

Note that the four sequences/structures must be of equal length, and that the structures induced by the gapped positions in their corresponding sequence must be a valid secondary structure.

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<applet  code="VARNA.class" codebase="bin" archive="VARNA.jar">
	<param name="comparisonMode" value="true" />
	<param name="firstSequence"
		value="CGCGCACGCGA....UAUU....UCGCGUCGCGCAUUUGCGCGUAGCGCG" />
	<param name="firstStructure"
		value="(((((.(((((............))))).(((((....)))))..)))))" />
	<param name="secondSequence"
		value="CGCGCACGCGSGCGCGUUUGCGCUCGCGU...............AGCGCG" />
	<param name="secondStructure"
		value="(((((.(((((((((....))))))))).................)))))" />
</applet>