3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
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 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/>.
18 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 <title>Nucleic Acid Support</title>
22 <style type="text/css">
25 font-family: "Courier New", Courier, mono;
34 <strong>Nucleic Acid Support</strong>
37 <em>Colour Schemes</em>
39 <p>Jalview has color schemes for nucleic acid based sequences,
40 ability to fetch sequences from RFAM and RNA secondary structure
43 Information on the <a href="../colourSchemes/nucleotide.html">Nucleotide
44 colour scheme</a> and <a href="../colourSchemes/purinepyrimidine.html">
45 Purine/Pyrimidine colour scheme</a> are available under the Colour Menu.
46 See <a href="../colourSchemes/index.html">Colour Schemes</a>.
51 Jalview supports annotation of RNA sequences with secondary structure
52 information. You can interactively
53 <a href="../features/annotation.html#rna">create and edit RNA
54 secondary structure annotation rows</a>, or import data in the following
57 <li><em>RFAM</em> - Sequences can be <a
58 href="../features/seqfetch.html">fetched</a> from the RFAM database
59 by accession number or ID.</li>
60 <li><em>Stockholm files</em> - WUSS (or VIENNA) dot-bracket
61 notation found in the secondary structure annotation line will be
62 imported as sequence or alignment associated secondary structure
64 <li><em>Clustal files</em> - certain RNA alignment programs, such
65 as <a href="http://rna.informatik.uni-freiburg.de:8080/LocARNA.jsp">LocaRNA</a>
66 output consensus RNA secondary structure lines in the line normally
67 reserved for the Clustal consensus line in a clustal file.</li>
68 <!-- <li><em>RNAML</em> - (coming soon) - Jalview can import RNAML files containing sequences and extended secondary structure annotation derived from RNA 3D structure</li> -->
71 <strong>RNA Secondary Structure Visualization and Analysis</strong><br />
72 If a sequence or RNA alignment has secondary structure information,
73 the alignment will have a secondary structure line shown below it, and
74 a number of additional options become available:
76 <li><a href="../colourschemes/rnaHelicesColouring.html">RNA
77 Helix colouring</a> - highlights columns of alignment involved in
78 particular RNA helices.</li>
79 <li><a href="../calculations/structureconsensus.html">Base Pair
80 Conservation Analysis</a> - shown as a histogram and base-pair logo
81 below the alignment.</li>
82 <li><a href="../features/varna.html">2D Structure
83 Visualization in VARNA</a> - allows linked viewing of the consensus or
84 an individual sequence's structure</li>
86 <p><strong>Limitations when working with RNA in Jalview</strong><br/>
87 Currently, Jalview is not able to export RNA secondary structure annotation in any format other than Jalview annotation
89 <em>Jalview's RNA handling capabilities were introduced in v2.8</em>
91 <p align="center"> </p>