General Category >> Help and How-to >> primer export

Message started by iain on Apr 15th, 2011 at 10:14pm

Title: primer export
Post by iain on Apr 15th, 2011 at 10:14pm

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?




Title: Re: primer export
Post by Agu on Apr 16th, 2011 at 6:02pm
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 | )

Title: Re: primer export
Post by Ilya Flyamer on Sep 21st, 2011 at 4:54pm
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?

Title: Re: primer export
Post by Mikhail Fursov on Sep 23rd, 2011 at 7:14pm
Hi Ilya!

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

Title: Re: primer export
Post by Ilya Flyamer on Sep 24th, 2011 at 12:18am
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!

Title: Re: primer export
Post by Konstantin Okonechnikov on Sep 30th, 2011 at 7:42pm
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 | )

Title: Re: primer export
Post by Ilya Flyamer on Oct 1st, 2011 at 3:07pm
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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