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Preserve case in DNA sequence? (Read 1615 times)
Nov 7th, 2015 at 2:20pm

Jens   Offline
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Posts: 7
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.
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Reply #1 - Nov 9th, 2015 at 1:31pm

German Grekhov   Offline
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Gender: male
Posts: 118
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".

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Reply #2 - Sep 19th, 2016 at 6:11pm

ClayAnderson2   Offline
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Posts: 5
thank you
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Reply #3 - Jan 31st, 2017 at 3:28pm

Motion Range   Offline
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Posts: 1
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
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