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Message started by hoytpr on Nov 25th, 2014 at 6:15am

Title: Problem importing .gbk files annotations
Post by hoytpr on Nov 25th, 2014 at 6:15am
Hello, When I open a multi-sequence .gbk file in UGENE, only a few of the sequences are loaded with annotations. For example a draft genome of a bacteria with 65 contigs, all annotated, but only 5 or 6 of the contigs show up with annotations. I can then add the other sequences to the VIEW by right-clicking and manually adding, but I wonder why all my annotations are not detected when I open the file?
Thanks!
Peter

Title: Re: Problem importing .gbk files annotations
Post by Olga Golosova on Nov 25th, 2014 at 3:13pm
Hello Peter!

Am I correct that you would like to work with all 65 contigs at the same time? Have you tried opening them as a single sequence (see the image below)?

Note that when you open sequences separately, only a few of them are loaded by default in the current UGENE version (1.14.2). In this case annotations of the OPENED sequences are only shown in the Annotations Editor. However, besides other sequences you can add the annotations objects to the VIEW as well. Feel free to ask any additional questions, if my descriptions is not clear enough.
reading_options.png (32 KB | 484 )

Title: Re: Problem importing .gbk files annotations
Post by hoytpr on Jan 28th, 2015 at 10:33pm
Hi Olga,
Thanks for the reply. I would like to work with all 65 (or now 75) contigs at the same time. Joining them together is not good for me because the "joins" would create artificial sequences. Also, I want to export annotations for all sequences.
However, if this is not part of UGENE, I will continue to slowly add each contig individually.
Thanks again.

Peter

Title: Re: Problem importing .gbk files annotations
Post by hoytpr on Jan 28th, 2015 at 10:54pm
Olga,
I tried to open the .GBK file as you suggested but got this error (I added "UNIMARK   Annotations" to the header also):

[ERROR][09:51] Trying to recover from error: Unexpected annotation table! at D:\teamcity\work\ugene-snapshot-hotfix\src\corelibs\U2Formats\src\EMBLGenbankAbstractDocument.cpp:161

Any advice?

Title: Re: Problem importing .gbk files annotations
Post by Olga Golosova on Jan 29th, 2015 at 5:38pm

Quote:
I tried to open the .GBK file as you suggested but got this error (I added "UNIMARK   Annotations" to the header also):

[ERROR][09:51] Trying to recover from error: Unexpected annotation table! at D:\teamcity\work\ugene-snapshot-hotfix\src\corelibs\U2Formats\src\EMBLGenbankAbs
tractDocument.cpp:161

Indeed, there is currently an error. I've created UGENE-3960 issue in our is issue-tracker.

Title: Re: Problem importing .gbk files annotations
Post by Olga Golosova on Jan 29th, 2015 at 5:44pm

hoytpr wrote on Jan 28th, 2015 at 10:54pm:
Any advice?

It seems, that you should use the Workflow Designer. The way how to use it depends on your exact tasks.

1) If you need to visually browse all the sequences, you can split them into separate GenBank files using the Workflow Designer and work with each sequence one by one.
2) If you need to work with all annotations at once you can export them into one file using the Workflow Designer.

It would be faster to discuss the details on a webinar, if you like so.

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