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General Category >> Feature Requests >> Simple GUI feature to select primers with exact endpoints of the selected sequence
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Message started by Jens on May 23rd, 2020 at 1:51pm

Title: Simple GUI feature to select primers with exact endpoints of the selected sequence
Post by Jens on May 23rd, 2020 at 1:51pm
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.

Title: Re: Simple GUI feature to select primers with exact endpoints of the selected sequence
Post by Dmitrii Sukhomlinov on May 25th, 2020 at 6:09pm
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?

Title: Re: Simple GUI feature to select primers with exact endpoints of the selected sequence
Post by Jens on May 28th, 2020 at 3:34pm
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

Title: Re: Simple GUI feature to select primers with exact endpoints of the selected sequence
Post by Dmitrii Sukhomlinov on May 29th, 2020 at 2:55pm
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?

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