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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
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* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
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+ -->
<head>
<title>Nucleic Acid Support</title>
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</style>
</head>
<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>
- 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> - (coming soon) - 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>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>
+ <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>
+
+ <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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