3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
\r
4 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
\r
6 * This file is part of Jalview.
\r
8 * Jalview is free software: you can redistribute it and/or
\r
9 * modify it under the terms of the GNU General Public License
\r
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
\r
12 * Jalview is distributed in the hope that it will be useful, but
\r
13 * WITHOUT ANY WARRANTY; without even the implied warranty
\r
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
\r
15 * PURPOSE. See the GNU General Public License for more details.
\r
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
\r
20 <title>The VARNA RNA Viewer</title>
\r
23 <p><strong>The VARNA RNA Viewer</strong></p>
\r
25 2.7.1, <a href="http://varna.lri.fr/index.html">VARNA</a> has been
\r
26 integrated into Jalview for interactively viewing structures opened by
\r
27 selecting the <strong>"Structure→View
\r
28 Structure:"</strong> option in
\r
29 the <a href="../menus/popupMenu.html">sequence id pop-up menu</a> (if
\r
30 you can't see this, then no RNA structure is associated with your
\r
31 sequence or alignment. In the pop-up menu all structures that
\r
32 are associated with this sequence and all sequences that are
\r
33 associated with the alignment are available.
\r
35 <p><strong>Different structures</strong></p>
\r
38 <b>Alignment structures</b>:
\r
39 Structures associated with the alignment are marked by having "consensus" attached to their name. VARNA contains two different entries for consensus structures.
\r
41 <li>Consensus structure: the individual sequence folded into the consensus structure</li>
\r
42 <li>Trimmed consensus structure: the individual sequence
\r
43 folded into the the gap-free consensus structure. That means all
\r
44 columns that contained gaps in the individual sequence were
\r
45 removed. If this breaks a base-pair the pairing is removed also.
\r
46 This can be considered as an approximation for the individual structure.
\r
50 <b>Individual structures</b>:
\r
51 this is a structure associated with the individual sequence and therefore not related to the alignment
\r
54 <p><strong>Controls</strong><br>
\r
56 <li>Rotate view - Left Click and drag</li>
\r
57 <li>Zoom in - Press '+'</li>
\r
58 <li>Zoom out - Press '-'</li>
\r
59 <li>Choose a different structure - Left click on structure in the left hand panel</li>
\r
60 <li>Highlighting bases - Move mouse over columns in the Jalview alignment panel</li>
\r
63 <p><strong>Functionality provided by VARNA</strong></p>
\r
64 <p>VARNA's own functions are accessed by right-clicking in the
\r
65 structure display area. That will open the VARNA pop-up menu,
\r
66 which provides access to a number of features like different draw algorithm, color highlighting or annotations.
\r
68 <p><strong>More Information</strong></p>
\r
69 <p>VARNA is a very powerful RNA viewer on its own. Only the
\r
70 essentials have been described here - the interested reader is
\r
71 referred to <a href="http://varna.lri.fr/usermanual.html">VARNA's own
\r
72 comprehensive online documentation</a>.</p>
\r