<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><italic>e.g. an active site residue</italic></li>\r
- <li>Features which span a region are coloured blue<br>\r
-<italic>e.g. a region of sequence with known structure</italic>\r
-</li>\r
-</ul></p>\r
-<p>More information about the feature is given in a tooltip, which are\r
- viewed by moving the mouse pointer over a sequence feature. The\r
- associated text for the feature will then be displayed in a small\r
- label will appear 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 must first determine if a\r
- sequence is contained in uniprot and then retrieve its sequence\r
- record. This delay should only happen once for a particular\r
- alignment, as jalview caches uniprot records in a file in your home\r
- directory called '.jalview.uniprot.xml'.\r
-\r
-<p>The first step in this process is to try to use the ID (name) of\r
- each sequence as an ID search in Uniprot. If there is no match, The\r
- EBI Blast search is used in an attempt to obtain the Uniprot Id for\r
- each sequence. You will be notified of any 100% matches with\r
- Uniprot, but you must then manually change the name of the sequence,\r
- by right clicking on the sequence ID and selecting\r
- Sequence→Edit Name, 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
-<p>\r
- If a uniprot record (or set of records) is found for a sequence,\r
- then the sequence in aligned to the one in the Uniprot record\r
- to determine the correct start and end residue positions that will be\r
- displayed when the 'Show Full Sequence ID' option is set.</p>\r
+<p><strong>Sequence Features</strong></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