Sequence Features
-This displays Uniprot sequence features on the alignment if a 100% sequence - match is found.
-The first step in this process is to match the id (name) of each sequence with - Uniprot. If there is no match, a Blast search is performed to try to obtain - the Uniprot Id for each sequence. You will be notified of any 100% matches with - Uniprot, which you must manually assign to each sequence in your input alignment, - then save the file.
+View→Sequence Features
+When this option is selected, sequence features extracted from the Uniprot + record for each sequence are displayed on the alignment.
+Jalview will attempt to retrieve sequence features from Uniprot files using + the EBI dbFetch web service using the given sequence names. A 100% match with + the Uniprot record is required to view the Sequence Features. If the match is + not 100%, Jalview will run EBI web service WUBlast to find unknown sequences. + You will be asked whether to proceed with this step, as it can take some time, + especially if the EBI servers are busy.
+More information about the feature is given in a tooltip, which is + viewed by moving the mouse pointer over a sequence feature. The + description associated with the feature will then be displayed in a small + label near the pointer.
+View→Feature Settings... +
Once sequence features have been loaded onto an alignment features can be hidden
+ or have their rendering priority changed using the Feature Settings dialog.
+ This displays all the features loaded, the colour and whether to display the
+ feature or not. You can easily change the colour by clicking the colour box.
+ It is important to realise that the order in which features are drawn to the
+ alignment may result in overlapping features being hidden. Features at the foot
+ of the table are rendered first. Therefore features higher up the table will
+ be drawn over the top of lower featrues. You can change the order of the feature
+ priority by dragging the feature with your mouse.
+ Use the transparency setting as another way to visualise overlapping features.
+
You can save all features, with their current colours and visibility + in a Jalview format file. +
The Sequence Identification Process + +
+The first step in the procedure for matching uniprot IDs to + sequences is to use the ID (name) of + each sequence to retrieve Uniprot records directly.
- The input sequence will be matched with the returned Uniprot record, the start - and end residues can then be correctly assigned to each sequence.
-Sequence features which are 1 residue in length are coloured red. Features - which span a region are coloured blue.
-By moving the mouse pointer over a sequence feature on the alignment a small - label will appear with the description of that sequence feature.
-A local cache of retrieved uniprot entries is recorded on your local machine. + If a uniprot record (or set of records) is found for a sequence, + then the sequence is aligned to the one in the Uniprot record + to determine the correct start and end residue positions (which are + displayed when the 'Show Full Sequence ID' option is set).
+ +If the alignment reveals differences between the sequence in the + alignment and the one in the record, then Jalview will assume that + the aligned sequence is not the one in the uniprot record. + +
+ ++ In some cases, the ID used to retrieve Uniprot records may be out of + date and you will be notified of that a 100% match between the + sequence and a Uniprot record was identified, but the sequence name + must be manually changed (by right clicking on the sequence ID and selecting + Sequence→Edit Name), before Jalview will show its sequence + features.