<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>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\r
+ controlled using the alignment window's <a\r
+ href="featuresettings.html">Sequence Feature Settings</a> dialog\r
+ box. Feature colour schemes and display parameters are unique to a\r
+ particular alignment, so it is possible to colour the same sequence\r
+ features differently in different alignment views.</p>\r
+<p><strong>View→Fetch Sequence Features</strong></p>\r
+<p>When this option is selected, sequence features extracted from the\r
+ <a href="http://www.ebi.uniprot.org/index.html">Uniprot (http://www.ebi.unprot.org/index.html)</a>\r
+ record for each sequence are displayed on the alignment.</p>\r
+<p>Jalview will attempt to retrieve sequence features from Uniprot files using\r
+ the EBI dbFetch web service using the given sequence names (or\r
+ Uniprot ID, if available). A 100% match with\r
+ the Uniprot record is required for Uniprot features to be view on a sequence.</p>\r
+<p>More information about the feature is given in a tooltip, which is viewed by\r
+ moving the mouse pointer over a sequence feature. The description associated\r
+ with the feature will then be displayed in a small label near the pointer.</p>\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
- 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
+ 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.\r
+<ul>\r
+ <li>remember to save your alignment if you have updated any of the sequence\r
+ IDs! </li>\r
+</ul>\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
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