How can I apply existing sequence features without re-creating them?


I am using Jalview (or trying to!) to add sequence features to my multiple alignment.

When I right-click a residue selection, I can choose to “create” a new sequence feature.

However, how can I apply an existing sequence feature without creating it all over again?

So, purely for example, let’s say that I have an alignment with 40 homologous enzymes. In my first sequence, I want to mark helix-hairpin-helix motifs manually as a sequence feature with a specific colour:

I select the appropriate range in the first sequence, right-click and add a new “helix hairpin helix” feature in purple.

Then I change to a different labelling task and decide that I want to label the active site as a sequence feature in this first sequence. I duly do so as before.

Now, I decide that I want to continue with the remaining thirty-nine sequences. I want to select specific ranges individually in each sequence and apply the helix-hairpin-helix feature again. However, I cannot find how to apply the existing feature - it has to be recreated and the name and colour has to be matched. Surely there is a list somewhere of features already applied to the project with a control to re-apply that feature to a new sequence segment?

Again, am I missing something? :slight_smile:

Thank you


Hi Michael,

You’re not missing something - except an enhanced ‘create feature’ interface that allows you to select from existing feature definitions.

We have a feature request about this already: - I’ll add your vote for it!

It is not quite what you want, but if you are adding a lot of features to an alignment, you might find it easier to create a “features file” to do this rather than using the graphical interface. Features files can be dropped on an alignment window to apply the features to the alignment.

There are some instructions here that may help.