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.
-- 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.
Sequence Features
+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.