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-<head>
-<title>Nucleic Acid Support</title>
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- <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/LocARNA">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>
-
- <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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