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License: GNU General Public License v3.0
Primer3Plus is an advanced web interface for primer3.
License: GNU General Public License v3.0
Hi there,
I was wondering if it would be possible to add a REST API for the primer3 web app or if that has been thought of before. It would be really useful!
Thanks
I want to design primer pairs while spanning an exon-exon junction through primer3plus.
when I determine my exon boundary as a target and also highlight some nucleotide of adjacent exons as an included region(around 5 nucleotides from each adjacent exon) it expresses "Too many included regions" and when I just determine my exon boundary as a target it dies not give me any primer pairs. Surprisingly, when I do the design with the NCBI, I have a bunch of primer pair suggestions. can anyone help me how to overcome this problem in primer3plus?
thank you in advanced
Hi,
I have use the setting file
primer3plus_2_4_2_default_settings.txt
with primer3core (command line version) and I don't have the same result than the web version (http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi).
have you done some modifications ?
Thanks.
Hi,
previous versions of primer3 allowed to pass parameters to the web interface through the URL, like this:
This was very useful to integrate primer3 into other tools so that the user does not have to copy the sequence manually.
Is there a reason this functionality was removed and could it maybe come back?
thanks for your help and your great work.
Hello!
I am building a private primer3plus web tool on apache2. But I don't find the cgi file and cgi folder, I want to know how to get them? Due to server limitations, I cannot use flask.
Hello,
I've installed a Primer3plus website from this git repository.
But when, for example, I run the "Check Primer" task the results (and the interface also) are quite different.
Sequence: aatcatcatacgac
Using www.bioinformatics.nl
Length: | 14 bp
Tm: | 32.0 °C
GC: | 35.7 %
ANY: | 4.0
SELF: | 2.0
3' Stability: | 7.8 ΔG
Using my web site
Length: | 14 bp
Tm: | 37.8 C
GC: | 35.7 %
Any Dimer: | 0.0
End Dimer: | 0.0
Template Mispriming: | 3.0
Hairpin: | 0.0
3' Stability: | 4.3 ΔG
Penalty: | 28.204
I can see that on the sourceforge web site (https://sourceforge.net/p/primer3/primer3plus/ci/master/tree/) there are some commit (related to Bugs Found by Heidelberg Bioinformatics Course) that are not present here in this git repository.
It is possible to merge those versions? Do I need to submit a PR?
How can I get the same results as www.bioinformatics.nl web site?
thank you.
Hi there,
I am using Primer3Plus version 3.3.0 and I am frequently running into problems when trying to design primer pairs with internal hybridization oligos.
To me it seems impossible to set a Hyb Oligo Penalty Weight other than 0. If I do set the penalty to e.g. 1, the task runs forever and doesn't finish.
Also the "pick primer list" task doesn't seem to work for me when trying to select an internal oligo alongside primers.
If I remember correctly, these things used to work fine 1-2 years ago before primer3plus was updated.
Is this a known issue?
Am I missing something?
Best, Martin
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