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:

• Features associated with a particular residue are coloured red
  e.g. an active site residue
• Features which span a region are coloured blue
  e.g. a region of sequence with known structure

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.

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

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.