3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
4 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
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 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 <title>The VARNA RNA Viewer</title>
23 <p><strong>The VARNA RNA Viewer</strong></p>
24 <p><a href="http://varna.lri.fr/index.html">VARNA</a> was
25 integrated into Jalview 2.8 to allow interactive viewing of RNA secondary structure annotation. It is opened by
26 selecting the <strong>"Structure→View
27 Structure:"</strong> option in
28 the <a href="../menus/popupMenu.html">sequence id pop-up menu</a> (if
29 you can't see this, then no RNA structure is associated with your
30 sequence or alignment. In the pop-up menu all structures that
31 are associated with this sequence and all sequences that are
32 associated with the alignment are available.
34 <p><strong>Different structures</strong></p>
37 <b>Alignment structures</b>:
38 Structures associated with the alignment are marked by having "consensus" attached to their name. VARNA contains two different entries for consensus structures.
40 <li>Consensus structure: the individual sequence folded into the consensus structure</li>
41 <li>Trimmed consensus structure: the individual sequence
42 folded into the the gap-free consensus structure. That means all
43 columns that contained gaps in the individual sequence were
44 removed. If this breaks a base-pair the pairing is removed also.
45 This can be considered as an approximation for the individual structure.
49 <b>Individual structures</b>:
50 this is a structure associated with the individual sequence and therefore not related to the alignment
53 <p><strong>Controls</strong><br>
55 <li>Rotate view - Left Click and drag</li>
56 <li>Zoom in - Press '+'</li>
57 <li>Zoom out - Press '-'</li>
58 <li>Choose a different structure - Left click on structure in the left hand panel</li>
59 <li>Highlighting bases - Move mouse over columns in the Jalview alignment panel</li>
62 <p><strong>Functionality provided by VARNA</strong></p>
63 <p>VARNA's own functions are accessed by right-clicking in the
64 structure display area. That will open the VARNA pop-up menu,
65 which provides access to a number of features like different draw algorithm, color highlighting or annotations.
67 <p><strong>More Information</strong></p>
68 <p>VARNA is a very powerful RNA viewer on its own. Only the
69 essentials have been described here - the interested reader is
70 referred to <a href="http://varna.lri.fr/usermanual.html">VARNA's own
71 comprehensive online documentation</a>.</p>