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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
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+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
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* The Jalview Authors are detailed in the 'AUTHORS' file.
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<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>
+ <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>
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