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