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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 />
<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
+ particular RNA helices, Uses the first displayed secondary structure annotation.</li>
+ <li><a href="../calculations/structureconsensus.html">Base Pair
Conservation Analysis</a> - shown as a histogram and base-pair logo
- below the alignment.</li>
+ below the alignment. Uses the first displayed secondary structure annotation row.</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>
+ an individual sequence's structure. Accessed via the Sequence ID popup menu.</li>
+ <li><strong>per sequence secondary structure
+ annotation</strong><br /> Sequence associated secondary structure
+ annotation imported via stockholm, PDB files, or other sources can
+ be shown on the alignment with the <strong>Colours→By
+ Annotation</strong> dialog box. Colours are assigned according to RNA
+ helix topology number (number of distinct nested helices).
+ Alignments can also be sorted by RNA helix secondary structure
+ topology number, <em>via</em> the <strong>Calculations→Sort→By
+ Annotation→Secondary Structure</strong> option (only present when
+ per-sequence secondary structure is available).</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