<html>\r
<head><title>Sequence Features</title></head>\r
<body>\r
-<p><strong>View→Sequence Features</strong></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\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/">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 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
+ <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>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
+<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 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
+ 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
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