<html>\r
+<head><title>Sequence Features</title></head>\r
<body>\r
<p><strong>Sequence Features</strong></p>\r
-<p>This displays Uniprot sequence features on the alignment if a 100% sequence\r
- match is found. </p>\r
-<p>The first step in this process is to match the id (name) of each sequence with\r
- Uniprot. If there is no match, a Blast search is performed to try to obtain\r
- the Uniprot Id for each sequence. You will be notified of any 100% matches with\r
- Uniprot, which you must manually assign to each sequence in your input alignment,\r
- then save the file.</p>\r
-<p>\r
- The input sequence will be matched with the returned Uniprot record, the start\r
- and end residues can then be correctly assigned to each sequence. </p>\r
-<p>Sequence features which are 1 residue in length are coloured red. Features\r
- which span a region are coloured blue. </p>\r
-<p>By moving the mouse pointer over a sequence feature on the alignment a small\r
- label will appear with the description of that sequence feature.</p>\r
-<p>A local cache of retrieved uniprot entries is recorded on your local machine.\r
-</p>\r
+<p>Jalview can colour parts of a sequence based on the presence of\r
+sequence features - which may be retrieved from database records (such\r
+as Uniprot), the result of <a href="search.html">sequence motif\r
+searches</a> or simply read from a <a\r
+href="featuresFormat.html">sequence features file</a>.</p>\r
+<p><strong>Sequence Feature Groups</strong></p>\r
+<p>Since Jalview 2.08, sequence features assigned to a sequence can be\r
+organised into groups, which may indicate that the features were all retrieved\r
+from the same database (such as Uniprot features), or generated by the\r
+same analysis process (as might be specified in a <a\r
+href="featuresFormat.html">sequence features file</a>).</p>\r
+<p><strong>Sequence Feature Inheritance</strong></p>\r
+<p>Since Jalview 2.08, sequence features are <em>global</em> to a set of\r
+sequences appearing (independently or together) in many different\r
+alignments. Practically, this means features loaded onto one alignment\r
+can be viewed in any alignments involving the same sequences. The same\r
+sequence appears in different alignments when a new alignment is\r
+generated by submitting an existing set of sequences to one of the\r
+alignment or prediction web services, and when sequences are copied\r
+and pasted into other alignment windows.</p>\r
+<p><strong>View→Show Sequence Features</strong></p>\r
+<p>Toggle the display of sequence features in this alignment. If\r
+feature retrieval has not already been carried out, then Jalview will\r
+automatically try to fetch sequence features (as described below).</p>\r
+<p><strong>View→Sequence Feature Settings...</strong>\r
+<p>Once sequence features have been loaded, their display can be fully controlled \r
+ using the alignment window's <a\r
+ href="featuresettings.html">Sequence Feature Settings</a> dialog box. Feature \r
+ colour schemes and display parameters are unique to a particular alignment, \r
+ so it is possible to colour the same sequence features differently in different \r
+ alignment views.<br>\r
+ Since Jalview 2.1, it is possible to add <a href="dassettings.html">DAS features</a> \r
+ to an alignment via the DAS tabbed pane of the feature settings window. </p>\r
+<p>Precalculated Sequence Features may be added to an alignment from the command\r
+ line, drag and drop, or from the "File->Load Features / Annotations"\r
+ menu item. See the <a href="featuresFormat.html">Features File Format</a> for\r
+ more details.</p>\r
</body>\r
</html>\r
git://source.jalview.org / jalview.git / blobdiff