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.
-- 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. -
+Jalview can colour parts of a sequence based on the presence of +sequence features - which may be retrieved from database records (such +as Uniprot), the result of sequence motif +searches or simply read from a sequence features file.
+Sequence Feature Groups
+Since Jalview 2.08, sequence features assigned to a sequence can be +organised into groups, which may indicate that the features were all retrieved +from the same database (such as Uniprot features), or generated by the +same analysis process (as might be specified in a sequence features file).
+Sequence Feature Inheritance
+Since Jalview 2.08, sequence features are global to a set of +sequences appearing (independently or together) in many different +alignments. Practically, this means features loaded onto one alignment +can be viewed in any alignments involving the same sequences. The same +sequence appears in different alignments when a new alignment is +generated by submitting an existing set of sequences to one of the +alignment or prediction web services, and when sequences are copied +and pasted into other alignment windows.
+View→Show Sequence Features
+Toggle the display of sequence features in this alignment. If +feature retrieval has not already been carried out, then Jalview will +automatically try to fetch sequence features (as described below).
+View→Sequence Feature Settings... +
Once sequence features have been loaded, their display can be fully controlled
+ using the alignment window's Sequence Feature Settings dialog box. Feature
+ colour schemes and display parameters are unique to a particular alignment,
+ so it is possible to colour the same sequence features differently in different
+ alignment views.
+ Since Jalview 2.1, it is possible to add DAS features
+ to an alignment via the DAS tabbed pane of the feature settings window.
Precalculated Sequence Features may be added to an alignment from the command + line, drag and drop, or from the "File->Load Features / Annotations" + menu item. See the Features File Format for + more details.