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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
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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> 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>Pseudo-knots</strong><br/>
+ Jalview 2.8.2 introduced limited support for working with structures including pseudoknots. Where possible, extended WUSS symbols (e.g. different types of parentheses, or upper and lower case letters) are preserved when parsing RNA structure annotation and will be shaded differently when displayed in the structure.<br/>
+ Extended WUSS annotation is also employed to distinguish different base pair interactions obtained from RNAML files.</p>
+
+ <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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