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General Category >> Feature Requests >> Save as a genbank (or embl, etc) file
http://ugene.net/forum/YaBB.pl?num=1241969209

Message started by big T on May 10th, 2009 at 10:26pm

Title: Save as a genbank (or embl, etc) file
Post by big T on May 10th, 2009 at 10:26pm
Hi, thanks for this cool program. I have used Artemis for updating my sequence annotations. Compared to Artemis, Ugene appears easier for mol biologists and provides convenient tools like a restriction analysis. I will recommend my labmates to try this.

However, I would like to see an option of saving new annotations as a new GenBank file, etc. It seems that current version (1.4.1) only allows export as a fasta format. If there's a way to do this, please let me know. Thanks.

Title: Re: Save as a genbank (or embl, etc) file
Post by Ivan Efremov on May 12th, 2009 at 7:33pm
Hi big T,


Quote:
However, I would like to see an option of saving new annotations as a new GenBank file, etc.

Any new annotations in UGENE appear as a part of a some new file. Just select it in Project View and click "save a copy" or "save selected" in context menu.


See attached images.

If you still have any questions please describe the way you creating new annotations.

new_annotation.png (30 KB | )
saving_document.png (35 KB | )

Title: Re: Save as a genbank (or embl, etc) file
Post by big T on May 13th, 2009 at 12:48am
Thanks, Ivan. Your suggestion helped me to find out a right way.


Quote:
If you still have any questions please describe the way you creating new annotations.


At first, the way you said didn't give me a complete Genbank file (see image 1). But when I make a new copy of the original Genbank file (which I want to modify) by "save a copy.." menu, a lock icon with the new document (see red arrowheads in image 2) is gone. Now I make a  new annotation on the new document "test.gb", save the new document, and it has a new annotation as well as the sequence (image 3).

Apparently eliminating the "lock" icon (i.e. making a document editable) solved the problem. Post any simpler solutions.
1_009.png (80 KB | )
2_008.png (113 KB | )
3_002.png (185 KB | )

Title: Re: Save as a genbank (or embl, etc) file
Post by big T on May 13th, 2009 at 12:58am
And creating a new document is reasonable in that I can have an old and new versions of a Genbank file. :)

Title: Re: Save as a genbank (or embl, etc) file
Post by Ivan Efremov on May 13th, 2009 at 12:53pm
big T, you found exactly the right way to append new annotations to existing documents.

In fact, UGENE cannot modify documents which were created by other tools. Instead UGENE has following models for working with new annotations: saving them as a new distinct file, which contains annotations only (the way I described) and creating a modifiable copy of the original file (the way you found).

Also, if you are interested in modifying original files see http://ugene.unipro.ru/forum/YaBB.pl?num=1238829036

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