The VARNA RNA Viewer

VARNA was integrated into Jalview 2.8 to allow interactive viewing of RNA secondary structure annotation. It is opened by selecting the "Structure→View Structure:" option in the sequence id pop-up menu (if you can't see this, then no RNA structure is associated with your sequence or alignment). In the pop-up menu all structures that are associated with this sequence and all sequences that are associated with the alignment are available.

Saving a Jalview session as a project file includes the state of any Varna viewers, which are reopened when the project is reloaded (since Jalview 2.9).

Different structures

• Alignment structures: Structures associated with the alignment are marked by having "consensus" attached to their name. VARNA contains two different entries for consensus structures.
  • Consensus structure: the individual sequence folded into the consensus structure
  • Trimmed consensus structure: the individual sequence folded into the the gap-free consensus structure. That means all columns that contained gaps in the individual sequence were removed. If this breaks a base-pair the pairing is removed also. This can be considered as an approximation for the individual structure.
• Individual structures: this is a structure associated with the individual sequence and therefore not related to the alignment

Controls

• Rotate view - Left Click and drag
• Zoom in - Press '+'
• Zoom out - Press '-'
• Choose a different structure - Left click on structure in the left hand panel
• Highlighting bases - Move mouse over columns in the Jalview alignment panel

Functionality provided by VARNA

VARNA's own functions are accessed by right-clicking in the structure display area. That will open the VARNA pop-up menu, which provides access to a number of features like different draw algorithm, color highlighting or annotations.

More Information

VARNA is a very powerful RNA viewer on its own. Only the essentials have been described here - the interested reader is referred to VARNA's own comprehensive online documentation.