matt,
I suppose that this problem could be solved with workflow designer, but need some more details.
could you please clarify your request a little bit?

what particular steps do you perform in your task? (like search for DNA pattern, primer etc.)
could you give an example of query "feature-list" to be executed on a sequence?

exactely.
My departement is working with gentle and pdraw32- but i somehow try ugene for my stuff first.
Just as Sebastian said - i meant the auto annotation of DNA features of the Sequence you´re working with.
So for example - if you start working with a quite common vector - you can add features - like promotor regions, selection cassettes, primers etc. once - and than simply "scan" new added sequences for those features instead of annotating each one for itself.

Another example - describing my case (means: beside a feature section for common annotation features (like in the example above - stuff that is used in several labs) it would be great to introduce my own features - which fit to my current project)
In my case it is for a common cloning project where:
1. i start with the gene of interest
2. use the cDNA for creating a vector including parts of it
3. introduce a selection cassette and amplify
4. use the amplified vector for transformation
So on each step several features are the same - so it would make things easier to enter annotations to a list or something similar once - and then simply "scan" your sequence of choice for those.

Hope you got what i mean.
Guess most wishes here lead to features similar to gentle, pdraw, serial cloner, ape and in special probably vectorNti