-<html>\r
-<head><title>Sequence Features</title></head>\r
-<body>\r
-<p><strong>View→Sequence Features</strong></p>\r
-<p>When this option is selected, sequence features extracted from the\r
- <a href="http://www.ebi.uniprot.org/">Uniprot</a> record for each\r
- sequence are displayed on the alignment.</p>\r
-<p>Currently, sequence features are rendered in red or blue, dependent\r
- upon their type:</p><ul>\r
- <li>Features associated with a particular residue are coloured\r
- red<br><em>e.g. an active site residue</em></li>\r
- <li>Features which span a region are coloured blue<br>\r
-<em>e.g. a region of sequence with known structure</em>\r
-</li>\r
-</ul></p>\r
-<p>More information about the feature is given in a tooltip, which is\r
- viewed by moving the mouse pointer over a sequence feature. The\r
- description associated with the feature will then be displayed in a small\r
- label near the pointer.</p>\r
-<p>After the Sequence Features option is selected, there may be some delay before\r
- the features are actually rendered, as jalview first determines if\r
- the sequences are contained in Uniprot and then retrieves any sequence\r
- records. This delay will normally only happen once for a particular\r
- set of sequences, as jalview caches uniprot records in a file in your home\r
- directory called '.jalview.uniprot.xml'.\r
-\r
- <p><strong>The Sequence Identification Process</strong>\r
-\r
- </p>\r
-<p>The first step in the procedure for matching uniprot IDs to\r
- sequences is to use the ID (name) of\r
- each sequence to retrieve Uniprot records directly.</p>\r
-<p>\r
- If a uniprot record (or set of records) is found for a sequence,\r
- then the sequence is aligned to the one in the Uniprot record\r
- to determine the correct start and end residue positions (which are\r
- displayed when the 'Show Full Sequence ID' option is set).\r
-</p>\r
-\r
-<p>If the alignment reveals differences between the sequence in the\r
- alignment and the one in the record, then Jalview will assume that\r
- the aligned sequence is not the one in the uniprot record.\r
-\r
- </p>\r
-\r
- <p> \r
- In some cases, the ID used to retrieve Uniprot records may be out of\r
- date and you will be notified of that a 100% match between the\r
- sequence and a Uniprot record was identified, but the sequence name\r
- must be manually changed (by right clicking on the sequence ID and selecting\r
- <strong>Sequence→Edit Name</strong>), before Jalview will show its sequence\r
- features.<ul>\r
- <li>remember to save your alignment if you have updated any of the\r
- sequence IDs!\r
- </li>\r
- </ul></p>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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>Sequence Features</title>
+</head>
+<body>
+<p><strong>Sequence Features</strong></p>
+<p>Jalview can colour parts of a sequence based on the presence of
+sequence features - which may be retrieved from database records (such
+as Uniprot), the result of <a href="search.html">sequence motif
+searches</a> or simply read from a <a href="featuresFormat.html">sequence
+features file</a>. You can also <a href="creatinFeatures.html">create
+features</a> from the results of searches or the current selection, and <a
+ href="editingFeatures.html">edit features</a> by double clicking on
+them.</p>
+<p><strong>Sequence Feature Colouring Styles</strong></p>
+<p>By default, Jalview will assign a color to each feature based on
+its type. These colours can be changed from the <a
+ href="featuresettings.html">feature settings</a> and <a
+ href="editingFeatures.html">amend features</a> dialog boxes. Since
+Jalview 2.5, it is also possible to define <a href="featureschemes.html">feature
+colourschemes</a> to shade features based on their associated scores or text
+labels.</p>
+<p><strong>Sequence Feature Groups</strong></p>
+<p>Since Jalview 2.08, sequence features assigned to a sequence can
+be organised into groups, which may indicate that the features were all
+retrieved from the same database (such as Uniprot features), or
+generated by the same analysis process (as might be specified in a <a
+ href="featuresFormat.html">sequence features file</a>).</p>
+<p><strong>Sequence Feature Inheritance</strong></p>
+<p>Since Jalview 2.08, sequence features are <em>global</em> to a
+set of sequences appearing (independently or together) in many different
+alignments. Practically, this means features loaded onto one alignment
+can be viewed in any alignments involving the same sequences. The same
+sequence appears in different alignments when a new alignment is
+generated by submitting an existing set of sequences to one of the
+alignment or prediction web services, and when sequences are copied and
+pasted into other alignment windows.</p>
+<p><strong>View→Show Sequence Features</strong></p>
+<p>Toggle the display of sequence features in this alignment. If
+feature retrieval has not already been carried out, then Jalview will
+automatically try to fetch sequence features (as described below).</p>
+<p><strong>View→Sequence Feature Settings...</strong></p>
+<p>Once sequence features have been loaded, their display can be
+fully controlled using the alignment window's <a
+ href="featuresettings.html">Sequence Feature Settings</a> dialog box.
+Feature colour schemes and display parameters are unique to a particular
+alignment, so it is possible to colour the same sequence features
+differently in different alignment views.<br>
+Since Jalview 2.1, it is possible to add <a href="dassettings.html">DAS
+features</a> to an alignment via the DAS tabbed pane of the feature settings
+window.</p>
+<p><strong>View→Sequence ID Tooltip→Show
+Non-Positional features</strong><br>
+<em>Only available in application</em></br>
+</p>
+<p>Toggles the display of non-positional features in the sequence ID
+tooltip, and whether they will be included when sequence features are
+exported using "File→Export Features".</p>
+<p>Precalculated Sequence Features may be added to an alignment from
+the command line, drag and drop, or from the "File→Load
+Features / Annotations" menu item. See the <a
+ href="featuresFormat.html">Features File Format</a> for more details.</p>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff