Hello, Antoine,
> 1. About the format of features: Name tab category(but not use by ugene during detection) tab and sequence. It's right? Because adding a feature doesn't work.
As you may see in the header of the "plasmid_features.txt" file (see 1.jpg), it has 3 fields - Feature (the annotation name), Type (Promoter, Terminaotor, Gene, Regulatory, Origin, Primer, or, if the type is dyfferent from the previous 5 types, it would be marked as Other features) and Sequence (sequence itself). These fields are separated with the TAB symbol. I suggest you just to copy one line (for example, the last one), paste this line to the end of file and replace fields you need to replace. I just tried and it works, you may add as many new features as you want.
The only problem which may appear is that your computer could prevent file saving due to lack of administrative rights. It would happen if, for example, you use Windows and UGENE is installed to "C:\Program Files\Unipro UGENE". In this case, you shoud modify you rights to allow you to write to this directory.
> 2. How, from a well (genbank) annotated sequences, add "automatically" features in plasmid_features.txt file.
Unfortunately, we do not have a such feature. The only way is to modify this file manually. It should be noted, that this feature didn't supposed to show any features user want, just some pre-defined (you may pay attention, that the "plasmid_features.txt" file has a link to the site these sites are came from
http://www.addgene.org/tools/reference/plasmid-features/).
> 3. This detection is strict, it could be possible to have a less strict detection ?
No, plasmid features could be found only in a strict way. You may use the "Search pattern" feature if you want to have more flexible search parameters.
We do not have plans in implementing features from points 2 and 3 from you reply in the nearest future, but if you are very interesting in them, it is necessary to say, that we have a commersial support for UGENE. If you are interested in this kind of cooperation, please, take us know and we will send you a commersial support offer.
Best regards,
Dmitrii Sukhomlinov,
The UGENE team.
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