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add annotation in Plasmid_features.txt (Read 419 times)
Sep 20th, 2023 at 4:43pm

ANTOINE   Offline
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Hello,
I want to improve automatic features detection on plasmid.
I have readed that all is in plasmid_features.txt but I failed to add a feature. So my questions are:
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.
2- How, from a well (genbank) annotated sequences, add "automatically" features in plasmid_features.txt file.
3- This detection is strict, it could be possible to have a less strict detection ?
Thanks for your help
Antoine 
 
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Reply #1 - Sep 20th, 2023 at 5:46pm

Dmitrii Sukhomlinov   Offline
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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.
 

1_001.jpg (23 KB | 20 )
1_001.jpg

Best regards,
Dmitrii Sukhomlinov,
The UGENE team.
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Reply #2 - Sep 20th, 2023 at 8:00pm

ANTOINE   Offline
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France

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Thanks Dmitrii for your very quick answer.

I have try your suggestion, and it'works perfectly. Maybe also I need to restart ugene.
For automatic addition, maybe I can try a semi-manually with the csv export of annotations... I will try this when I have time to waste.
For commercial support, It's a pertinent suggestion. I have no Idea of the cost, and above all of the administrative implication (I need to check because I am in  public research center). Another question, we can choose to use a commercial support and to share the result with all Ugene users (as sponsoring the developpement of specific ugene tools)?
Thanks for your response
Antoine
 
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Reply #3 - Oct 2nd, 2023 at 3:36pm

evelin   Offline
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ANTOINE wrote on Sep 20th, 2023 at 8:00pm:
Thanks Dmitrii for your very quick answer.

I have try your suggestion, and it'works perfectly. Maybe also I need to restart ugene.
For automatic addition, maybe I can try a semi-manually with the csv export of annotations... I will try this when I have time to waste.
For commercial support, It's a pertinent suggestion. I have no Idea of the cost, and above all of the administrative implication (I need to check because I am in  public research center). Another question, we can choose to use a commercial support and to share the result with all Ugene users (as sponsoring the developpement of specific ugene tools)?
Thanks for your response
Antoine


Hello. Please ask us this commercial support question at ugene@unipro.ru

Thank you for using UGENE: you make us better!
 
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