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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 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
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<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>
-
+ <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, 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. 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. 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>
-</div>
-<p align="center"> </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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