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  UGENE Forum › General Category › Help and How-to › Testing internal Primers with Primer3
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Testing internal Primers with Primer3 (Read 3299 times)
Sep 10th, 2020 at 3:35pm

viniciuspr   Offline
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Hi everyone,

I am new with UGene and I would like to test some primers with my DNA sequence. I designed the primers using NCBI tool and I had inserted it into UGENE primer library.
However, I have not found any option to test my internal oligo with this software.

Does anyone know how to test internal oligos (probes/taqman) using UGENE?

Thanks in advance

Best Wishes

Vinicius
 
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Reply #1 - Sep 12th, 2020 at 1:37pm

Dmitrii Sukhomlinov   Offline
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The only way to use UGENE primer library is located in Sequence View in the "In Silico PCR" tab. There is a little button called "Choose a primer from the primer library" forward and reverse primers (see the attached picture). Click on the button and choose primer from the ibrary.
 
Screenshot_2.png (74 KB | 291 )
Screenshot_2.png
Best regards,
Dmitrii Sukhomlinov,
The UGENE team.
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Reply #2 - Sep 17th, 2020 at 2:45am

viniciuspr   Offline
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Dear Dimitrii,

Thank you very much for your helpful reply.
I see the in silico PCR tab and the options you mentioned, however, it is still not possible to add a third sequence, in this case, the internal oligo (probe).

Best Regards

Vinicius


Dmitrii Sukhomlinov wrote on Sep 12th, 2020 at 1:37pm:
The only way to use UGENE primer library is located in Sequence View in the "In Silico PCR" tab. There is a little button called "Choose a primer from the primer library" forward and reverse primers (see the attached picture). Click on the button and choose primer from the ibrary.

 
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Reply #3 - Sep 17th, 2020 at 11:05am

Dmitrii Sukhomlinov   Offline
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I'm not sure... Do you want the third sequence primer for "In Silico PCR"? And what kind of results do you want to get?
 
Best regards,
Dmitrii Sukhomlinov,
The UGENE team.
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