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23 <title>The VARNA RNA Viewer</title>
26 <p><strong>The VARNA RNA Viewer</strong></p>
27 <p><a href="http://varna.lri.fr/index.html">VARNA</a> was
28 integrated into Jalview 2.8 to allow interactive viewing of RNA secondary structure annotation. It is opened by
29 selecting the <strong>"Structure→View
30 Structure:"</strong> option in
31 the <a href="../menus/popupMenu.html">sequence id pop-up menu</a> (if
32 you can't see this, then no RNA structure is associated with your
33 sequence or alignment). In the pop-up menu all structures that
34 are associated with this sequence and all sequences that are
35 associated with the alignment are available.
36 <p>Saving a Jalview session as a project file includes the state of any Varna viewers, which are reopened when the project is reloaded <em>(since Jalview 2.9)</em>.
38 <p><strong>Different structures</strong></p>
41 <b>Alignment structures</b>:
42 Structures associated with the alignment are marked by having "consensus" attached to their name. VARNA contains two different entries for consensus structures.
44 <li>Consensus structure: the individual sequence folded into the consensus structure</li>
45 <li>Trimmed consensus structure: the individual sequence
46 folded into the the gap-free consensus structure. That means all
47 columns that contained gaps in the individual sequence were
48 removed. If this breaks a base-pair the pairing is removed also.
49 This can be considered as an approximation for the individual structure.
53 <b>Individual structures</b>:
54 this is a structure associated with the individual sequence and therefore not related to the alignment
57 <p><strong>Controls</strong><br>
59 <li>Rotate view - Left Click and drag</li>
60 <li>Zoom in - Press '+'</li>
61 <li>Zoom out - Press '-'</li>
62 <li>Choose a different structure - Left click on structure in the left hand panel</li>
63 <li>Highlighting bases - Move mouse over columns in the Jalview alignment panel</li>
66 <p><strong>Functionality provided by VARNA</strong></p>
67 <p>VARNA's own functions are accessed by right-clicking in the
68 structure display area. That will open the VARNA pop-up menu,
69 which provides access to a number of features like different draw algorithm, color highlighting or annotations.
71 <p><strong>More Information</strong></p>
72 <p>VARNA is a very powerful RNA viewer on its own. Only the
73 essentials have been described here - the interested reader is
74 referred to <a href="http://varna.lri.fr/index.php?page=manual&css=varna">VARNA's own
75 comprehensive online documentation</a>.</p>