View→Sequence Features
-When this option is selected, sequence features extracted from the - Uniprot record for each - sequence are displayed on the alignment.
-Currently, sequence features are rendered in red or blue, dependent - upon their type:
More information about the feature is given in a tooltip, which are +
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 - associated text for the feature will then be displayed in a small - label will appear near the pointer.
-After the Sequence Features option is selected, there may be some delay before - the features are actually rendered, as jalview must first determine if a - sequence is contained in uniprot and then retrieve its sequence - record. This delay should only happen once for a particular - alignment, as jalview caches uniprot records in a file in your home - directory called '.jalview.uniprot.xml'. + 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 this process is to try to use the ID (name) of - each sequence as an ID search in Uniprot. If there is no match, The - EBI Blast search is used in an attempt to obtain the Uniprot Id for - each sequence. You will be notified of any 100% matches with - Uniprot, but you must then manually change the name of the sequence, - by right clicking on the sequence ID and selecting - Sequence→Edit Name, before Jalview will show its sequence +
+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.
++ 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.
- If a uniprot record (or set of records) is found for a sequence, - then the sequence in aligned to the one in the Uniprot record - to determine the correct start and end residue positions that will be - displayed when the 'Show Full Sequence ID' option is set.