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.
+Currently, sequence features are rendered in red or blue, dependent + upon their type:
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.
+After the Sequence Features option is selected, there may be some delay before + the features are actually rendered, as jalview first determines if + the sequences are contained in Uniprot and then retrieves any sequence + records. This delay will normally only happen once for a particular + set of sequences, as jalview caches uniprot records in a file in your home + directory called '.jalview.uniprot.xml'. + +
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.