3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
4 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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>Nucleic Acid Support</title>
21 <style type="text/css">
24 font-family: "Courier New", Courier, mono;
32 <p><strong>Nucleic Acid Support</strong></p>
33 <p><em>Colour Schemes</em></p>
34 <p>Jalview has color schemes for nucleic acid based sequences, ability to
35 fetch sequences from RFAM and RNA secondary structure coloring</p>
36 <p>Information on the <a href="../colourSchemes/nucleotide.html">Nucleotide
37 colour scheme</a> and <a href="../colourSchemes/purinepyrimidine.html">
38 Purine/Pyrimidine colour scheme</a> are available
39 under the Colour Menu. See <a href="../colourSchemes/index.html">Colour
41 <p><em>RNA Support</em></p>
42 <p>Sequences can be <a href="../features/seqfetch.html">fetched</a> from the
43 RFAM database by accession number or ID.</p>
44 <p>If an RNA alignment is loaded from a Stockholm file with secondary
45 structure information in WUSS notation, the alignment can be coloured by
46 the helices in the secondary structure. Helices are determined by the base-pairing
47 in the secondary structure line. See <a href="../colourSchemes/rnahelicesColouring.html">
48 RNA Helices Colouring</a>. Below is an example of this type of coloring</p>
49 <p>Annotation panel shows the presence of RNA helices and WUSS notation from
50 input file specifying secondary structure.<p>
52 <img src="../colourschemes/rnahelicescoloring.png" width="600" height="140"> </div>
56 <p align="center"> </p>