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annotations (Read 18061 times)

May 15^th, 2013 at 2:02am

piruvato Offline
YaBB Newbies

Posts: 3

Dear Ugene Team,

First of all, thank you very much for your great job, it is an excelent software. My suggestion could be not necessary but I thik is really usefull. Could you implement some kind of autoanotation for the most common features?

Thanks again

M

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Reply #1 - May 16^th, 2013 at 2:01am

Konstantin Okonechnikov Offline
Global Moderator

Posts: 173

Hi! Thanks for the kind words

What do you mean by "the most common features"? Could you please provide some examples?

There is actually a similar feature planned already:
https://ugene.unipro.ru/tracker/browse/UGENE-125

But its description should be improved and expanded with particular examples.

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Reply #2 - May 16^th, 2013 at 5:20pm

piruvato Offline
YaBB Newbies

Posts: 3

Thanks for your answer,

The features could be the ones taht are used frequently in plasmid construction, like AMP/NEO resistance, IRES, CMV promoter, ori, Loxp, frt, PolyA signal, 2A sequences, GFP Lacz..... and maybe indentify ORFs. Coluld be an option to retrieve information from databases to anotate.

I thnk this would be very usefull, but I understand that could be difficult to implement.

Miquel

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Reply #3 - Jun 28^th, 2013 at 10:07pm

piruvato Offline
YaBB Newbies

Posts: 3

Hello,

I find this web tool that may be interestion regarding to the autoanotations.

wishart.biology.ualberta.ca/PlasMapper/

Could be possible to link ugene with it to anotate?

Thanks

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Reply #4 - Oct 24^th, 2013 at 12:29am

Nex Offline
YaBB Newbies
UK

Posts: 6

Dear Ugene developers,

I absolutely agree with the previous poster, this would be an excellent feature to have. I look forward to see the auto-annotations improved as described on the planned feature.

I regularly use the NCBI website, but I have not seen it among the examples. Please check any of the Nucleotide or Protein pages. There, the sequences are highlighted and can be readily accessed, so they must have a powerful annotation feature behind. I was wondering if an annotations table from NCBI could be directly implemented in an editable version within UGENE? That would be fantastic.

Thank you for the big effort you are doing in UGENE, it is great software and very, very useful for the community!

Best regards,
Nex

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Reply #5 - Jul 25^th, 2014 at 4:57pm

Nex Offline
YaBB Newbies
UK

Posts: 6

Dear Ugene developers,

I wanted to add my support to refresh this feature request. An auto-annotation feature would be extremely useful.
Also I would like to add that it would be excellent to improve the import of .gb files from GenBank or vectorNTI, for the labels to show correctly in Ugene (e.g. see the 'gene name' and not 'CDS' on the maps)

Best regards,
Nex

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Reply #6 - Jul 25^th, 2014 at 9:07pm

Olga Golosova Offline
YaBB Administrator

Posts: 338

Dear all,

Thank you for your feedbacks!
In the upcoming UGENE version 1.14 we've implemented Plasmid Auto Annotation feature. The 1.14 UGENE version will come out in about a week and you're welcome to check it out!

As described in the documentation, the features for plasmids auto annotating were taken from the following resource: http://www.addgene.org/tools/reference/plasmid-features/

Currently, it is not possible to add features into this list using the UGENE GUI. Is this feature required?

If you need to add features into the list, you'll now have to manually edit the following file from the UGENE package: data/custom_annotations/plasmid_features.txt

Also, you can try out the feature from a snapshot and share your experience with us before the release, so we can tweak it: http://ugene.unipro.ru/snapshot.html

Kind regards,
Olga

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Reply #7 - Jul 25^th, 2014 at 9:25pm

Olga Golosova Offline
YaBB Administrator

Posts: 338

Dear Nex,

Quote:

I regularly use the NCBI website, but I have not seen it among the examples. Please check any of the Nucleotide or Protein pages. There, the sequences are highlighted and can be readily accessed, so they must have a powerful annotation feature behind. I was wondering if an annotations table from NCBI could be directly implemented in an editable version within UGENE? That would be fantastic.

Quote:

to improve the import of .gb files from GenBank

Could you please describe in more details what you mean. As far as I understand, GenBank files are submitted to NCBI by the community, so they do not annotate the files themselves. If I'm wrong and there is also some annotation table from NCBI, could you please provide me with the link?
The GenBank format is fully supported in UGENE. Do you experience some problems loading GenBank files?

Quote:

or vectorNTI

We'll take into account your request. There is already an issue in our issue-tracking system.

Quote:

for the labels to show correctly in Ugene (e.g. see the 'gene name' and not 'CDS' on the maps)

Please also provide more details about the problem. It should be OK by default. More exactly, a qualifier value must be shown on the annotations map. See https://ugene.unipro.ru/wiki/display/UUOUM/Captions+on+Annotations

Kind regards,
Olga

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