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https://forum.ugene.net/forum/YaBB.pl General Category >> Feature Requests >> Preserve case in DNA sequence? https://forum.ugene.net/forum/YaBB.pl?num=1446880857 Message started by Jens on Nov 7^th, 2015 at 2:20pm

Title: Preserve case in DNA sequence?
Post by Jens on Nov 7^th, 2015 at 2:20pm

I just tried to convert a PhD student in our unit to use Ugene instead of CLC workbench.

One of her problems was that she wanted to import a sequence with alternating upper-case and lower-case DNA sequences that represented exon and intron sequences.

Apparently, this works in CLC. I could not find such an option in UGene and I have no idea how generally useful this feature would be.

If possible another neat feature might be to be able to select sequence segments based on case.

Title: Re: Preserve case in DNA sequence?
Post by German Grekhov on Nov 9^th, 2015 at 1:31pm

Jens, the only thing I can suggest you is to switch on the lower/upper case annotations (see the documentation here: https://ugene.unipro.ru/wiki/pages/viewpage.action?pageId=16126576). Click the menu Settings -> Preferences, then choose the "File Format" section and choose "Use lower case annotations. After that the regions, that are written with a lower case in a file, will be annotated in UGENE with the annotation "lower_case"; and you can rename them manually to "intron".

2015-11-09_123123.png (41 KB | 550 )

Title: Re: Preserve case in DNA sequence?
Post by ClayAnderson2 on Sep 19^th, 2016 at 6:11pm

thank you

Title: Re: Preserve case in DNA sequence?
Post by Motion Range on Jan 31^st, 2017 at 3:28pm

I'm glad I found this post. I am used to CLC and I was thrown off course when I encountered this issue. This helped and the manual addition is quite okay. Thanks