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 are + 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'. + +
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 + features.
- 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 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.