3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
4 * Copyright (C) 2014 The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
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14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
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19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
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.
37 <p><strong>Different structures</strong></p>
40 <b>Alignment structures</b>:
41 Structures associated with the alignment are marked by having "consensus" attached to their name. VARNA contains two different entries for consensus structures.
43 <li>Consensus structure: the individual sequence folded into the consensus structure</li>
44 <li>Trimmed consensus structure: the individual sequence
45 folded into the the gap-free consensus structure. That means all
46 columns that contained gaps in the individual sequence were
47 removed. If this breaks a base-pair the pairing is removed also.
48 This can be considered as an approximation for the individual structure.
52 <b>Individual structures</b>:
53 this is a structure associated with the individual sequence and therefore not related to the alignment
56 <p><strong>Controls</strong><br>
58 <li>Rotate view - Left Click and drag</li>
59 <li>Zoom in - Press '+'</li>
60 <li>Zoom out - Press '-'</li>
61 <li>Choose a different structure - Left click on structure in the left hand panel</li>
62 <li>Highlighting bases - Move mouse over columns in the Jalview alignment panel</li>
65 <p><strong>Functionality provided by VARNA</strong></p>
66 <p>VARNA's own functions are accessed by right-clicking in the
67 structure display area. That will open the VARNA pop-up menu,
68 which provides access to a number of features like different draw algorithm, color highlighting or annotations.
70 <p><strong>More Information</strong></p>
71 <p>VARNA is a very powerful RNA viewer on its own. Only the
72 essentials have been described here - the interested reader is
73 referred to <a href="http://varna.lri.fr/usermanual.html">VARNA's own
74 comprehensive online documentation</a>.</p>