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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
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* This file is part of Jalview.
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* Jalview is free software: you can redistribute it and/or
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+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
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- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
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<head>
<title>Nucleic Acid Support</title>
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<body>
-<p><strong>Nucleic Acid Support</strong></p>
-<p><em>Colour Schemes</em></p>
-<p>Jalview has color schemes for nucleic acid based sequences, ability to
-fetch sequences from RFAM and RNA secondary structure coloring</p>
-<p>Information on the <a href="../colourSchemes/nucleotide.html">Nucleotide
-colour scheme</a> and <a href="../colourSchemes/purinepyrimidine.html">
-Purine/Pyrimidine colour scheme</a> are available
-under the Colour Menu. See <a href="../colourSchemes/index.html">Colour
-Schemes</a>.</p>
-<p><em>RNA Support</em></p>
-<p>Sequences can be <a href="../features/seqfetch.html">fetched</a> from the
-RFAM database by accession number or ID.</p>
-<p>If an RNA alignment is loaded from a Stockholm file with secondary
-structure information in WUSS notation, the alignment can be coloured by
-the helices in the secondary structure. Helices are determined by the base-pairing
-in the secondary structure line. See <a href="../colourSchemes/rnahelicesColouring.html">
-RNA Helices Colouring</a>. Below is an example of this type of coloring</p>
-<p>Annotation panel shows the presence of RNA helices and WUSS notation from
-input file specifying secondary structure.<p>
-<div align="center">
- <img src="../colourschemes/rnahelicescoloring.png" width="600" height="140"> </div>
-
-
-</div>
-<p align="center"> </p>
+ <p>
+ <strong>Nucleic Acid Support</strong>
+ </p>
+ <p>
+ <em>Colour Schemes</em>
+ </p>
+ <p>Jalview has color schemes for nucleic acid based sequences,
+ ability to fetch sequences from RFAM and RNA secondary structure
+ coloring</p>
+ <p>
+ Information on the <a href="../colourSchemes/nucleotide.html">Nucleotide
+ colour scheme</a> and <a href="../colourSchemes/purinepyrimidine.html">
+ Purine/Pyrimidine colour scheme</a> are available under the Colour Menu.
+ See <a href="../colourSchemes/index.html">Colour Schemes</a>.
+ </p>
+ <p>
+ <em>RNA Support</em>
+ </p>
+ Jalview supports annotation of RNA sequences with secondary structure
+ information. You can interactively
+ <a href="../features/annotation.html#rna">create and edit RNA
+ secondary structure annotation rows</a>, or import data in the following
+ way:
+ <ul>
+ <li><em>RFAM</em> - Sequences can be <a
+ href="../features/seqfetch.html">fetched</a> from the RFAM database
+ by accession number or ID.</li>
+ <li><em>Stockholm files</em> - WUSS (or VIENNA) dot-bracket
+ notation found in the secondary structure annotation line will be
+ imported as sequence or alignment associated secondary structure
+ annotation.</li>
+ <li><em>Clustal files</em> - certain RNA alignment programs, such
+ as <a href="http://rna.informatik.uni-freiburg.de:8080/LocARNA.jsp">LocaRNA</a>
+ output consensus RNA secondary structure lines in the line normally
+ reserved for the Clustal consensus line in a clustal file.</li>
+ <!-- <li><em>RNAML</em> - (coming soon) - Jalview can import RNAML files containing sequences and extended secondary structure annotation derived from RNA 3D structure</li> -->
+ </ul>
+ <p>
+ <strong>RNA Secondary Structure Visualization and Analysis</strong><br />
+ If a sequence or RNA alignment has secondary structure information,
+ the alignment will have a secondary structure line shown below it, and
+ a number of additional options become available:
+ <ul>
+ <li><a href="../colourschemes/rnaHelicesColouring.html">RNA
+ Helix colouring</a> - highlights columns of alignment involved in
+ particular RNA helices.</li>
+ <li><a href="../calculations/structureconsensus.html">Base Pair
+ Conservation Analysis</a> - shown as a histogram and base-pair logo
+ below the alignment.</li>
+ <li><a href="../features/varna.html">2D Structure
+ Visualization in VARNA</a> - allows linked viewing of the consensus or
+ an individual sequence's structure</li>
+ </ul>
+ <p><strong>Limitations when working with RNA in Jalview</strong><br/>
+ Currently, Jalview is not able to export RNA secondary structure annotation in any format other than Jalview annotation
+ </br>
+ <em>Jalview's RNA handling capabilities were introduced in v2.8</em>
+ </p>
+ <p align="center"> </p>
</body>
</html>
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