Hi, I really like UGENE and the workflow designer, but here is my problem:

I'm using HMM to annotate two features (s1, s2) in a sequence and would like to add a third annotation (K1) in between that starts at the end of s1 and goes until the beginning of s2. How can I do that? via a script?

Thanks  :)

Hi. I've been trying to do that as well for a long time. As far as I know there's no way to annotate something between two annotations (tried with query designer, but no success).

I will add that as a feature request as it should be very useful (https://ugene.unipro.ru/tracker/browse/UGENE-1331).

For now, you can annotate the whole region, including s1 and s2, using the "Collocation search" element (Basic Analysis group). The description is not very clear for me, but basically it will search for a series of annotations (s1 and s2) that must be inside a given maximum distance. But it will annotate the complete region as a new feature.

We have implemented the feature you suggest. You can download just released UGENE 1.11.4 and try it:
http://ugene.unipro.ru/download.html

You need to use "Collocation search" workflow element. The new option "Include boundaries" has been added. When you use "Create new annotations" result type and the option is false then your task will be resolved.
See attached screenshots.

Also, I have attached example.uwl workflow schema which you can try.

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