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https://forum.ugene.net/forum/YaBB.pl General Category >> Bugs and Issues >> Genebank format join errors https://forum.ugene.net/forum/YaBB.pl?num=1375293884 Message started by hoytpr on Aug 1^st, 2013 at 1:04am

Title: Genebank format join errors
Post by hoytpr on Aug 1^st, 2013 at 1:04am

When adding a genebank file (these were generated by RAST), there are problem with joining of the CDS lines. You cannot have the same sequence number used in a "join". Example:

CDS join(38563..38789,38791..38799) is okay but:
CDS join(38563..38789,38789..38799) is bad, and UGENE will NOT open the .gbk file.

Is this a problem with the RAST output or is it UGENE?

Windows XP-Pro x64
Two 4-core AMD opteron processors
UGENE 1.12.1 64-bit

Title: Re: Genebank format join errors
Post by German Grekhov on Aug 8^th, 2013 at 5:27pm

hoytpr, what version of UGENE do you use? I use UGENE 1.12.1. I have tried to open a file with such annotations and it is opened well. You can see the attached screenshot with the opened file.

If the version of UGENE you use is less then 1.12.1, please, download and install the latest one from our site: http://ugene.unipro.ru/download.html

If you use UGENE 1.12.1 and you can not open such files, could you try to open the attached file "try.gb", please? Also, in this case it will be great if you send us the file you can not open with UGENE. It would help to investigate the problem.

https://forum.ugene.net/forum/YaBB.pl?action=downloadfile;file=try.gb (174 KB | )

genbank.png (109 KB | )

Title: Re: Genebank format join errors
Post by hoytpr on Nov 25^th, 2014 at 6:23am

Wow, I took a long time to reply. I am able to open the try.gb file and get the same image you show using version 1.14.1 of UGENE. The file that was not opening, is lost now. I apologize.

Title: Re: Genebank format join errors
Post by German Grekhov on Nov 25^th, 2014 at 7:50pm

Hello, Peter. Thank you for your reply! It's great to hear that the file is opened well in your computer and you don't face this problem.

Looking forward for your further activity in the project's life :)

By the way, are you interested in participating in UGENE webinars? These webinars are free and their goal is to teach people to use UGENE effectively in solving their tasks.