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.

View→Fetch Sequence Features

When this option is selected, sequence features extracted from the Uniprot (http://www.ebi.unprot.org/index.html) 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 (or Uniprot ID, if available). A 100% match with the Uniprot record is required for Uniprot features to be view on a sequence.

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.

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.

• remember to save your alignment if you have updated any of the sequence IDs!

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.