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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
* Copyright (C) 2014 The Jalview Authors
*
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* Jalview is free software: you can redistribute it and/or
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+ * You should have received a copy of the GNU General Public License
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<head>
<title>Nucleic Acid Support</title>
<style type="text/css">
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> -->
+ <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 />
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>
git://source.jalview.org / jalview.git / blobdiff