<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></p>\r
-<p>More information about the feature is given in a tooltip, which are\r
+<p>When this option is selected, sequence features extracted from the <a href="http://www.ebi.uniprot.org/">Uniprot</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. A 100% match with \r
+ the Uniprot record is required to view the Sequence Features. If the match is \r
+ not 100%, Jalview will run EBI web service WUBlast to find unknown sequences. \r
+ You will be asked whether to proceed with this step, as it can take some time, \r
+ especially if the EBI servers are busy. </p>\r
+<p>More information about the feature is given in a tooltip, which is\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
+ description associated with the feature will then be displayed in a small\r
+ label near the pointer.</p>\r
+<p><strong>View→Feature Settings...</strong>\r
+<p>Once sequence features have been loaded onto an alignment features can be hidden \r
+ or have their rendering priority changed using the Feature Settings dialog. \r
+ This displays all the features loaded, the colour and whether to display the \r
+ feature or not. You can easily change the colour by clicking the colour box.<br>\r
+ It is important to realise that the order in which features are drawn to the \r
+ alignment may result in overlapping features being hidden. Features at the foot \r
+ of the table are rendered first. Therefore features higher up the table will \r
+ be drawn over the top of lower featrues. You can change the order of the feature \r
+ priority by dragging the feature with your mouse. <br>\r
+ Use the transparency setting as another way to visualise overlapping features. \r
+<p><strong><em>You can save all features, with their current colours and visibility \r
+ in a Jalview format file. </em></strong>\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
+ </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 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.<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
</body>\r
</html>\r
git://source.jalview.org / jalview.git / blobdiff