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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:
secondSequenceparameters to some string, using the dot '
.' character to denote gaps.
secondStructureparameters, 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>