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Simple GUI feature to select primers with exact endpoints of the selected sequence (Read 1355 times)
May 23rd, 2020 at 1:51pm

Jens   Offline
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A very common primer design use case is that you need primers with the exact end points of your selected sequence. I would propose a simple tick box to  select this case similar to how it is done in webprimer:

http://www.candidagenome.org/cgi-bin/compute/web-primer

The Primer3 method of giving starting coordinate and sequence length is not obvious and the interface is confusing where many students end up designing internal primers.
 
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Reply #1 - May 25th, 2020 at 6:09pm

Dmitrii Sukhomlinov   Offline
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Can you, please, specify more clearly your idea. As I understand, you want to add a new checkbox to the "Primer designer" dialog, which allows finding primers if, and only if, their endpoint is the same as the endpoint of the region you're picking primers at?
Also, you've mentioned the method of "giving starting coordinate and sequence length". Can you describe, what settings did you describe here?
 

Best regards,
Dmitrii Sukhomlinov,
UGENE team.
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Reply #2 - May 28th, 2020 at 3:34pm

Jens   Offline
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Indeed I mean a simple check box that forces the program to only design primers including the exact end points of the selected sequence, like in the simple webprimer interface I linked to in the previous post.

The way it is done now according to primer3 instructions is under the option "Targets"

http://bioinfo.ut.ee/primer3-0.4.0/primer3/primer3_www_help.html
 
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Reply #3 - May 29th, 2020 at 2:55pm

Dmitrii Sukhomlinov   Offline
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I think I've got your idea - the checkbox, which allows you to find primers if the endpoint of the reverse-complement primer is the same as the endpoint of the sequence, isn't it?
But let me get this right about the way of doing it with "Primer3" and "Targets" options. I'm' not pretty sure how this feature is supposed to be done by using the "Targets" option. For example, I have a sequence of 500 characters in length. What "Target" value should be set up, in this case, to make primers endpoints be the same as the sequence endpoint?
 

Best regards,
Dmitrii Sukhomlinov,
UGENE team.
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Reply #4 - Feb 18th, 2021 at 10:53pm

Leonardo   Offline
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I'm not sure if Primer3 add-on calculates primer hairpins. I know it calculates primer dimers. If it doesn't, here is my suggestion to incorporate this feature. I usually use IDTOligoAnalyzer Tool because of this: it's a complete analysis package despite the annoying need to create an account just to use their tool.

Another issue I've just noticed recently is the plugins section: almost all of the links posted lead to nowhere. I wanted to add a plugin to my UGene instalallation but was unable to because of it. Please fix the hyperlinks so they point to another web page where we can read about and download the plugin or alternatively begin downloading it right away.
 
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