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primer export (Read 9414 times)

Apr 15^th, 2011 at 10:14pm

iain Offline
YaBB Newbies

Posts: 1

Hi

I'm brand new to Ugene. I'm starting off with something simple and hopefully will work up to more complex projects as I get used to the software.

At the moment I'm using Ugene to design PCR primers and I'm wondering if there's an easy way to export primers to e.g. a spreadsheet?

Thanks.

best

i

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Reply #1 - Apr 16^th, 2011 at 6:02pm

Agu Offline
Junior Member
(Argentinian)

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Posts: 63

Hi!
Yes, you can export them. Once you have performed a search, all primers found will be in the annotations panel (bottom). Just right click in the ones or the full set of primers that you want to export and choose Export/Export annotations... Then you can choose comma separated values (csv), and then open that with your favourite spreadsheet program...
Remember to check the "Save sequences under annotations" mark.

screenshot1.png (128 KB | )

Screenshot2.png (19 KB | )

Screenshot3.png (67 KB | )

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Reply #2 - Sep 21^st, 2011 at 4:54pm

Ilya Flyamer Offline
Full Member

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Posts: 126

Hello!
I'm also new to ugene. I'm trying to make primers for PCR, but I don't get them. They do not appear as annotations, as you have shown above. I think, the program just can't find them, it's a rather narrow search. But, for example, PerlPrimer finds about 10 different primer pairs in the same case.
What could be the problem?

« Last Edit: Sep 21^st, 2011 at 8:48pm by Ilya Flyamer »

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Reply #3 - Sep 23^rd, 2011 at 7:14pm

Mikhail Fursov Offline
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Posts: 162

Hi Ilya!

Could you provide a sample data set, so we can analyze it and compare results with other problems?

---
UGENE team

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Reply #4 - Sep 24^th, 2011 at 12:18am

Ilya Flyamer Offline
Full Member

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Posts: 126

Hello, Mikhail!
Yes, sure.
NG_008308.1 - accession in ncbi. We need to design primers to amplify ORF: 16250-17399, but they shouldn't be too far from the ends of this fragment (not more, than 50-100 bp). Maybe I was just doing something wrongly, but I don't know...
Thanks in advance!
Ilya.

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Reply #5 - Sep 30^th, 2011 at 7:42pm

Konstantin Okonechnikov Offline
Global Moderator

Posts: 173

Ilya, I've investigated your case.
You should adjust proper options for primer search.

First of all, set the Target region, which you would like to amplify. It would be starting at 16250 with the size of approximately 1200
Then add product size range of 1500.
And there is also an option for maximum number of returned results, which is 5 by default.

I've attached a screenshot for your convenience.
You can read more about primer3 options here.

Primer_designer_props.png (73 KB | )

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Reply #6 - Oct 1^st, 2011 at 3:07pm

Ilya Flyamer Offline
Full Member

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Posts: 126

Thank you! Yes, it helped very much! The reason must have been, that I didn't point the product size, just deleted suggested numbers.

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