<mapID target="colours.abovepid" url="html/colourSchemes/abovePID.html"/>
<mapID target="colours.conservation" url="html/colourSchemes/conservation.html"/>
<mapID target="colours.annotation" url="html/colourSchemes/annotationColouring.html"/>
+ <mapID target="colours.purinepyrimidine" url="html/colourSchemes/purinepyrimidine.html"/>
+ <mapID target="colours.rnahelices" url="html/colourSchemes/rnahelicesColouring.html"/>
<mapID target="calcs.alquality" url="html/calculations/quality.html"/>
<mapID target="calcs.alconserv" url="html/calculations/conservation.html"/>
<mapID target="calcs.consensus" url="html/calculations/consensus.html"/>
+ <mapID target="nucleicAcids" url="html/na/index.html"/>
+
<mapID target="menus" url="html/menus/index.html"/>
<mapID target="desktopMenu" url="html/menus/desktopMenu.html"/>
<mapID target="alMenu" url="html/menus/alignmentMenu.html"/>
--- /dev/null
+<html><head><title>Jalview - Help </title></head>
+<body bgcolor=#F1F1F1>
+<p><center><strong>Contents</strong></center></p>
+
+<br><a href="html/index.html" target=bodyframe>Jalview Documentation</a>
+<br> <a href="html/whatsNew.html" target=bodyframe>What's new</a>
+<br> <a href="html/features/featureschemes.html" target=bodyframe>Graduated Feature Colours</a>
+<br> <a href="html/features/featuresettings.html" target=bodyframe>Sort by Features</a>
+<br> <a href="html/webServices/index.html" target=bodyframe>Envision2 Service</a>
+<br> <a href="html/releases.html" target=bodyframe>Release History</a>
+<br> <a href="html/editing/index.html" target=bodyframe>Editing Alignments</a>
+<br> <a href="html/features/cursorMode.html" target=bodyframe>Cursor Mode</a>
+<br> <a href="html/keys.html" target=bodyframe>Key Strokes</a>
+<br> <a href="html/io/index.html" target=bodyframe>Input / Output</a>
+<br> <a href="html/io/export.html" target=bodyframe>Making Figures</a>
+<br> <a href="html/features/hiddenRegions.html" target=bodyframe>Hidden Regions</a>
+<br> <a href="html/features/multipleViews.html" target=bodyframe>Multiple Views</a>
+<br> <a href="html/calculations/treeviewer.html" target=bodyframe>Viewing Trees</a>
+<br> <a href="html/features/seqfetch.html" target=bodyframe>Fetching Sequences</a>
+<br> <a href="html/features/seqfeatures.html" target=bodyframe>Sequence Features</a>
+<br> <a href="html/features/featuresettings.html" target=bodyframe>Sequence Feature Settings</a>
+<br> <a href="html/features/featuresFormat.html" target=bodyframe>Sequence Features File</a>
+<br> <a href="html/features/featureschemes.html" target=bodyframe>Feature Colourschemes</a>
+<br> <a href="html/features/creatinFeatures.html" target=bodyframe>User Defined Sequence Features</a>
+<br> <a href="html/features/editingFeatures.html" target=bodyframe>Editing Sequence Features</a>
+<br> <a href="html/features/dasfeatures.html" target=bodyframe>DAS Feature Retrieval</a>
+<br> <a href="html/features/dassettings.html" target=bodyframe>DAS Feature Settings</a>
+<br> <a href="html/webServices/index.html" target=bodyframe>Web Services</a>
+<br> <a href="html/webServices/msaclient.html" target=bodyframe>Sequence Alignment</a>
+<br> <a href="html/webServices/clustalw.html" target=bodyframe>Clustal Alignment</a>
+<br> <a href="html/webServices/muscle.html" target=bodyframe>Muscle Alignment</a>
+<br> <a href="html/webServices/mafft.html" target=bodyframe>MAFFT Alignment</a>
+<br> <a href="html/webServices/msaclient.html" target=bodyframe>Multiple Alignment Subjobs</a>
+<br> <a href="html/webServices/jnet.html" target=bodyframe>Secondary Structure Prediction</a>
+<br> <a href="html/features/seqfetch.html" target=bodyframe>Sequence Retrieval</a>
+<br> <a href="html/webservices/dbreffetcher.html" target=bodyframe>Database Reference Retrieval</a>
+<br> <a href="html/features/dasfeatures.html" target=bodyframe>DAS Feature Retrieval</a>
+<br> <a href="html/na/index.html" target=bodyframe>Nucleic Acid Support</a>
+<br> <a href="html/colourSchemes/index.html" target=bodyframe>Colour Schemes</a>
+<br> <a href="html/colourSchemes/textcolour.html" target=bodyframe>Background Dependent Text Colour</a>
+<br> <a href="html/colourSchemes/clustal.html" target=bodyframe>ClustalX</a>
+<br> <a href="html/colourSchemes/zappo.html" target=bodyframe>Zappo</a>
+<br> <a href="html/colourSchemes/taylor.html" target=bodyframe>Taylor</a>
+<br> <a href="html/colourSchemes/hydrophobic.html" target=bodyframe>Hydrophobicity</a>
+<br> <a href="html/colourSchemes/helix.html" target=bodyframe>Helix propensity</a>
+<br> <a href="html/colourSchemes/strand.html" target=bodyframe>Strand propensity</a>
+<br> <a href="html/colourSchemes/turn.html" target=bodyframe>Turn propensity</a>
+<br> <a href="html/colourSchemes/buried.html" target=bodyframe>Buried index</a>
+<br> <a href="html/colourSchemes/nucleotide.html" target=bodyframe>Nucleotide colours</a>
+<br> <a href="html/colourSchemes/purinepyrimidine.html" target=bodyframe>Purine/Pyrimidine colours</a>
+<br> <a href="html/colourSchemes/blosum.html" target=bodyframe>Blosum62</a>
+<br> <a href="html/colourSchemes/pid.html" target=bodyframe>by Percentage Identity</a>
+<br> <a href="html/colourSchemes/user.html" target=bodyframe>User Defined</a>
+<br> <a href="html/colourSchemes/abovePID.html" target=bodyframe>Above Percentage Identity</a>
+<br> <a href="html/colourSchemes/conservation.html" target=bodyframe>By conservation</a>
+<br> <a href="html/colourSchemes/annotationColouring.html" target=bodyframe>By Annotation</a>
+<br> <a href="html/colourSchemes/rnahelicesColouring.html" target=bodyframe>By RNA Helices</a>
+<br> Calculations
+<br> <a href="html/calculations/sorting.html" target=bodyframe>Sorting alignments</a>
+<br> <a href="html/calculations/tree.html" target=bodyframe>Calculating trees</a>
+<br> <a href="html/calculations/pca.html" target=bodyframe>Principal Component Analysis</a>
+<br> <a href="html/calculations/recoverInputdata.html" target=bodyframe>Tree/PCA Input Data</a>
+<br> <a href="html/calculations/pairwise.html" target=bodyframe>Pairwise Alignments</a>
+<br> <a href="html/calculations/redundancy.html" target=bodyframe>Remove Redundancy</a>
+<br> <a href="html/features/annotation.html" target=bodyframe>Alignment Annotations</a>
+<br> <a href="html/calculations/conservation.html" target=bodyframe>Conservation</a>
+<br> <a href="html/calculations/quality.html" target=bodyframe>Quality</a>
+<br> <a href="html/calculations/consensus.html" target=bodyframe>Consensus</a>
+<br> <a href="html/features/annotationsFormat.html" target=bodyframe>Annotations File Format</a>
+<br> <a href="html/features/viewingpdbs.html" target=bodyframe>Viewing PDB Files</a>
+<br> <a href="html/features/jmol.html" target=bodyframe>Jmol Viewer</a>
+<br> <a href="html/features/pdbviewer.html" target=bodyframe>Simple PDB Viewer</a>
+<br> <a href="html/vamsas/index.html" target=bodyframe>VAMSAS Data Exchange</a>
+<br> <a href="html/menus/index.html" target=bodyframe>Window Menus</a>
+<br> <a href="html/menus/desktopMenu.html" target=bodyframe>Desktop Window</a>
+<br> <a href="html/menus/alignmentMenu.html" target=bodyframe>Alignment Window</a>
+<br> <a href="html/menus/alwfile.html" target=bodyframe>File Menu</a>
+<br> <a href="html/menus/alwedit.html" target=bodyframe>Edit Menu</a>
+<br> <a href="html/menus/alwselect.html" target=bodyframe>Select Menu</a>
+<br> <a href="html/menus/alwview.html" target=bodyframe>View Menu</a>
+<br> <a href="html/menus/alwformat.html" target=bodyframe>Format Menu</a>
+<br> <a href="html/menus/alwcolour.html" target=bodyframe>Colour Menu</a>
+<br> <a href="html/menus/alwcalculate.html" target=bodyframe>Calculation Menu</a>
+<br> <a href="html/menus/wsmenu.html" target=bodyframe>Web Service Menu</a>
+<br> <a href="html/menus/alwannotations.html" target=bodyframe>Annotation Menus</a>
+<br> <a href="html/menus/popupMenu.html" target=bodyframe>Popup Menu</a>
+<br> <a href="html/features/preferences.html" target=bodyframe>Preferences</a>
+<br> <a href="html/memory.html" target=bodyframe>Memory Settings</a>
+<br> <a href="html/jalviewjnlp.html" target=bodyframe>JNLP with extra memory parameters</a>
+<br> <a href="html/features/commandline.html" target=bodyframe>Command Line</a>
+<br> <a href="html/features/clarguments.html" target=bodyframe>Command Line Arguments</a>
+<br> <a href="html/features/groovy.html" target=bodyframe>Groovy Shell</a>
+<br> <a href="html/privacy.html" target=bodyframe>Privacy</a>
+<br>Useful information
+<br> <a href="html/misc/aminoAcids.html" target=bodyframe>Amino Acid Table</a>
+<br> <a href="html/misc/aaproperties.html" target=bodyframe>Amino Acid Properties</a>
+<br> <a href="html/misc/geneticCode.html" target=bodyframe>The Genetic Code</a>
<tocitem text="Multiple Views" target="multipleviews"/>
<tocitem text="Viewing Trees" target="treeviewer" expand="false"/>
<tocitem text="Fetching Sequences" target="seqfetch"/>
+ <tocitem text="Nucleic Acid Support" target="nucleicAcids" expand="false"></tocitem>
<tocitem text="Sequence Features" target="seqfeatures" expand="false">
<tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>
<tocitem text="Sequence Features File" target="features.fileformat"/>
<tocitem text="Turn propensity" target="colours.turn"/>
<tocitem text="Buried index" target="colours.buried"/>
<tocitem text="Nucleotide colours" target="colours.nucleotide"/>
+ <tocitem text="Purine/Pyrimidine colours" target="colours.purinepyrimidine"/>
<tocitem text="Blosum62" target="colours.blosum"/>
<tocitem text="by Percentage Identity" target="colours.pid"/>
<tocitem text="User Defined" target="colours.user"/>
<tocitem text="Above Percentage Identity" target="colours.abovepid"/>
<tocitem text="By conservation" target="colours.conservation"/>
<tocitem text="By Annotation" target="colours.annotation"/>
+ <tocitem text="By RNA Helices" target="colours.rnahelices"/>
</tocitem>
<tocitem text="Calculations" target="calculations" expand="false">
<tocitem text="Sorting alignments" target="sorting"/>
<p>The default colour schemes are summarised in the table below:
<div align="center">
<p> </p>
+<p><strong>Protein Colour Schemes</strong></p>
<table border="1">
<tr>
<td>
</td>
</tr>
</table>
+<p> </p>
+<p><strong>Nucleotide Colour Schemes</strong></p>
+<table border="1">
+ <tr>
+ <td>
+ <table border="1">
+ <tr>
+ <td nowrap></td>
+ <td>A</td> <!--Adenine-->
+ <td>C</td> <!--Cytosine-->
+ <td>G</td> <!--Guanine-->
+ <td>T</td> <!--Thymine-->
+ <td>U</td> <!--Uracil-->
+ <td>I</td> <!--Inosine-->
+ <td>X</td> <!--Xanthine-->
+ <td>R</td> <!--Unknown Purine-->
+ <td>Y</td> <!--Unknown Pyrimidine-->
+ <td>N</td> <!--Unknown-->
+ <td>W</td> <!--Weak nucleotide (A or T)-->
+ <td>S</td> <!--Strong nucleotide (G or C)-->
+ <td>M</td> <!--Amino (A or C)-->
+ <td>K</td> <!--Keto (G or T)-->
+ <td>B</td> <!--Not A (G or C or T)-->
+ <td>H</td> <!--Not G (A or C or T)-->
+ <td>D</td> <!--Not C (A or G or T)-->
+ <td>V</td> <!--Not T (A or G or C-->
+ </tr>
+ <tr>
+ <td height="24">Nucleotide</td>
+ <td bgcolor="#64F73F"></td>
+ <td bgcolor="#FFB340"></td>
+ <td bgcolor="#EB413C"></td>
+ <td bgcolor="#3C88EE"></td>
+ <td bgcolor="#3C88EE"></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ </tr>
+ <tr>
+ <td height="24">Purine/Pyrimidine</td>
+ <td bgcolor="#FF83FA"></td>
+ <td bgcolor="#40E0D0"></td>
+ <td bgcolor="#FF83FA"></td>
+ <td bgcolor="#40E0D0"></td>
+ <td bgcolor="#40E0D0"></td>
+ <td></td>
+ <td></td>
+ <td bgcolor="#FF83FA"></td>
+ <td bgcolor="#40E0D0"></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ </tr>
+ </table>
+ </td>
+ </tr>
+</table>
+
+
</div>
<p align="center"> </p>
</body>
<td bgcolor="#FFB340">C</td>
<td bgcolor="#EB413C">G</td>
<td bgcolor="#3C88EE">T</td>
+ <td bgcolor="#3C88EE">U</td>
</tr>
</table>
</div>
--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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.
+ *
+ * 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/>.
+-->
+<head><title>Purine/Pyrimidine Colour Scheme</title>
+<style type="text/css">
+<!--
+td {
+ text-align: center;
+}
+-->
+</style>
+</head>
+
+<body>
+<p><em>Purine/Pyrimidine Colours</em></p>
+<div align="center">
+ <table width="200" border="1">
+ <tr>
+ <td bgcolor="#FF83FA">Purines <BR> A, G, R</td>
+ <td bgcolor="#40E0D0">Pyrimidines <BR> C, U, T, Y</td>
+ </tr>
+ </table>
+</div>
+</body>
+</html>
--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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.
+ *
+ * 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/>.
+-->
+<head><title>RNA Helices Colouring</title></head>
+
+<body>
+<p><strong> RNA Helices Colouring </strong></p>
+<p>An RNA alignment loaded from a Stockholm file can be coloured
+ based on its helices. The helices are determined from the
+ secondary structure line in the Stockholm file (#GC SS_cons)
+ written in WUSS notation
+ that specifies base pairing. See <a href="http://en.wikipedia.org/wiki/Stockholm_format">
+ Wikipedia</a> or <a href="http://jalview-rnasupport.blogspot.com/2010/06/parsing-wuss-notation-of-rna-secondary.html">
+ Jalview RNA Support Blog</a> for more information about Stockholm files and WUSS notation.</p>
+Select "Colour" <strong>→</strong> "
+ By RNA Helices" to colour the alignment by RNA helices. <br>
+ <br>
+<p><em>Features</em></p>
+<ul>
+<li>Colours are generated randomly for the number of helices present.
+Reselect the "By RNA Helices" option to generate another set of random colors. </li>
+<li>Sequence logo is in <a href="purinepyrimidine.html">
+Purine/Pyrimidine colour scheme</a>. </li>
+<li>Line above the "Secondary Structure" line in annotation panel is WUSS notation present
+in the input file.</li>
+</ul>
+
+
+
+ <div align="center">
+ <img src="rnahelicescoloring.png" width="600" height="140"> </div>
+
+
+</body>
+</html>
</head>
<body>
<p><strong>Sequence Fetcher</strong></p>
-<p>Jalview can retrieve sequences from certain databases using
-either the WSDBFetch service provided by the European Bioinformatics
-Institute, and, since Jalview 2.4, DAS servers capable of the <em>sequence</em>
-command (configured in <a href="dassettings.html">DAS settings</a>).</p>
-<img src="seqfetcher.gif" align="center"
- alt="The Jalview Sequence Fetcher Dialog Box">
-<p>The Sequence Fetcher dialog box can be opened via the
-"File" menu on the main desktop in order to retrieve sequences
-as a new alignment, or opened via the "File" menu of an
-existing alignment to import additional sequences. Please note, there
-will be a short delay when the sequence fetcher is first opened, whilst
-Jalview compiles the list of available sequence datasources from the
-currently defined DAS server registry.</strong></p>
-<p>First, select the database you want to retrieve sequences from.
-Then, enter one or more accession ids (as a semi-colon separated list),
-or press the "Example" button to paste the example accession
-for the currently selected database into the retrieval box. Finally,
-press "OK" to initiate the retrieval.</p>
-<p><em>Fetching Individual PDB Chains</em><br>
-If you are retrieving sequences from the PDB, you can retrieve specific
-chains by appending a colon and the chain id to the PDB id. For example
-:<br>
-<pre> 1GAQ:A</pre>
-</p>
-<p><em>Retrieving parts of large sequence records</em><br>
-When retrieving from DAS sequence sources, coordinate range arguments
-can be passed to the server using the standard DAS sequence command
-format:<pre>
- <AccessionId>:<start>,<end></pre> If you know a source
-understands this type of query format, then you should untick the
-checkbox for 'replace commas with semi-colons' so the range query can be
-passed to the server; otherwise, the query will be split into two (e.g
-'Mito:1' and '85779' rather than 'Mito:1,85779'). In most cases,
-however, a source that supports range queries will include a range
-qualification in its example query, and Jalview will then automatically
-disable the 'replace commas with semi-colons' option.<br>
-<em>The option to disable the comma to semi-colon translation was
-added in Jalview 2.6</em></p>
-<p>If you use the WSDBFetch sequence fetcher services (EMBL,
-Uniprot, PDB and PFAM) in work for publication, please cite:</p>
-<p>Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S.,
-Tate J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez
-R. <br>
-SOAP-based services provided by the European Bioinformatics Institute.<br>
-Nucleic Acids Res. 33(1):W25-W28 (2005) <br>
-<br>
+<p>Jalview can retrieve sequences from certain databases using either the
+WSDBFetch service provided by the European Bioinformatics Institute, and, since Jalview 2.4, DAS servers capable of the <em>sequence</em> command (configured in <a href="dassettings.html">DAS settings</a>).</p>
+<img src="seqfetcher.gif" align="center" alt="The Jalview Sequence Fetcher Dialog Box">
+<p>The Sequence Fetcher dialog box can be opened via the "File"
+ menu on the main desktop in order to retrieve sequences as a new
+ alignment, or opened via the "File" menu of an existing alignment
+ to import additional sequences. Please note, there will be a short delay when the sequence fetcher is first opened,
+ whilst Jalview compiles the list of available sequence datasources from the
+ currently defined DAS server registry.</strong>
</p>
+<p>First, select the database you want to retrieve sequences from. Then, enter
+ one or more accession ids (as a semi-colon separated list), or press the
+ "Example" button to paste the example accession for the currently selected database into the retrieval box.
+ Finally, press "OK" to initiate the retrieval.</p>
+<p>
+ If you are retrieving sequences from the PDB, you can retrieve
+ specific chains by appending a colon and the chain id to the PDB
+ id. For example :<br><pre> 1GAQ:A</pre><br>When retrieving from DAS sequence sources,
+ coordinate range arguments can be passed to the server using the standard DAS
+ sequence command format (<strong>:<start>,<end></strong>)</p>
+<p>If you use the WSDBFetch sequence fetcher services (EMBL, Uniprot, PDB, PFAM, and RFAM)
+ in work for publication, please cite:</p>
+<p>Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar
+ S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R. <br>
+ SOAP-based services provided by the European Bioinformatics Institute.<br>
+ Nucleic Acids Res. 33(1):W25-W28 (2005) <br>
+ <br>
+ </p>
</body>
</html>
</tr><tr><td width="17%">PFAM</td>
<td width="60%">SequenceName THISISASEQENCE</td>
<td width="23%">.pfam</td>
+</tr><tr>
+<td width="17%">Stockholm</td>
+<td width="60%"># STOCKHOLM VersionNumber<br>
+<em>...</em><br>//</td>
+<td width="23%">.stk, .sto</td>
</tr>
</table>
<p>The file extensions are used to associate jalview alignment icons
<ul>
<li><strong>Fetch Sequence</strong><br>
<em>Shows a dialog window in which you can select known ids from
- Uniprot, EMBL, EMBLCDS or PDB database using Web Services provided by
+ Uniprot, EMBL, EMBLCDS, PDB, PFAM, or RFAM databases using Web Services provided by
the European Bioinformatics Institute. See <a
href="../features/seqfetch.html">Sequence Fetcher</a></em>.</li>
<li><strong>Add Sequences</strong><em><br>
<li>Colour Scheme options: <strong>None, ClustalX,
Blosum62 Score, Percentage Identity, Zappo, Taylor, Hydrophobicity,
Helix Propensity, Strand Propensity, Turn Propensity, Buried Index,
- Nucleotide, User Defined<br>
+ Nucleotide, Purine/Pyrimidine, User Defined<br>
</strong> <em>See <a href="../colourSchemes/index.html">colours</a> for a
description of all colour schemes.</em><br>
</li>
annotation. See <a href="../colourSchemes/annotationColouring.html">Annotation
Colouring</a>.</em><br>
</li>
+ <li><strong>By RNA Helices</strong><br>
+ <em>Colours the helices of an RNA alignment loaded from a Stockholm file. See
+ <a href="../colourSchemes/rnahelicesColouring.html">RNA Helices
+ Colouring</a>.</em><br>
+ </li>
</ul>
</li>
<li><strong>Calculate</strong>
</em></li>
<li>Colour Scheme options: <strong>None, ClustalX, Blosum62 Score, Percentage
Identity, Zappo, Taylor, Hydrophobicity, Helix Propensity, Strand Propensity,
- Turn Propensity, Buried Index, Nucleotide, User Defined<br>
+ Turn Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User Defined<br>
</strong> <em>See <a href="../colourSchemes/index.html">colours</a> for
a description of all colour schemes.</em><br>
</li>
<em>Colours the alignment on a per-column value from a specified annotation.
See <a href="../colourSchemes/annotationColouring.html">Annotation Colouring</a>.</em><br>
</li>
+ <li><strong>By RNA Helices</strong><br>
+ <em>Colours the helices of an RNA alignment loaded from a Stockholm file. See
+ <a href="../colourSchemes/rnahelicesColouring.html">RNA Helices
+ Colouring</a>.</em><br>
+ </li>
</ul>
</body>
</html>
<ul>
<li><strong>Fetch Sequence</strong><br>
<em>Shows a dialog window in which you can select known ids from
- Uniprot, EMBL, EMBLCDS or PDB database using Web Services provided by
+ Uniprot, EMBL, EMBLCDS, PDB, PFAM, or RFAM databases using Web Services provided by
the European Bioinformatics Institute. See <a
href="../features/seqfetch.html">Sequence Fetcher</a></em>.</li>
<li><strong>Add Sequences</strong><em><br>
--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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.
+ *
+ * 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/>.
+-->
+<head>
+<title>Nucleic Acid Support</title>
+<style type="text/css">
+<!--
+td {
+ font-family: "Courier New", Courier, mono;
+ font-style: normal;
+ font-size: medium;
+}
+-->
+</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>
+<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>
+
+
+</div>
+<p align="center"> </p>
+</body>
+</html>
<li>Visualization of superposed structures associated with protein
or nucleotide sequence alignments.</li>
<li>Export coordinates and projection as CSV from PCA viewer</li>
+ <li>New Purine/Pyrimidine colour scheme</li>
+ <li>Colouring of RNA secondary structure by helices. See <a href="na/index.html">Nucleic Acid Support</a></li>
+
</ul>
<p><strong>Issues Resolved (a select list - see release
git://source.jalview.org / jalview.git / commitdiff
