primer3-org / primer3plus Goto Github PK

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

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.

Hi,
I installed prime3 and prime3plus according to the steps and started it. When accessing the web page, I was prompted No response from the server trying to load default settings from server. I do not know what caused this.

Can you give me some suggestions?

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,

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:

https://www.primer3plus.com/index.html?SEQUENCE_TEMPLATE=TCCGGCTCTGCTCCTGGCTGGGGGTCTCCTTGGCCTTCTTACAGGTGTACAGCCACTTGATGATGCGGGCGTTCCTCTCGATGACCGAAGTGGTGCTGGGCACCTGCTCTATCAGCTCCTCCTCCTGCAGCCCCTCGTCGTCGCCGCCGC%5BTGTGCCGGGAGAAGCCGCTGCCGGAGGTGGCGACGCTCACGCTGCGCACCTTGAGGGTCACACAGTCCGACCCCGCGGTGAAGTTCTCCCTCCCCAGGGCCTCCACCACCTCGGGGTCCAGGCCGCAGTACTGGAAGAAGGTGTCAGACTCGGCCAAGGCAGCGGAATAGCGGGAGCTGAGGTCCGACTGTGAGCGCTGCA%5DGCCCCCGACGCCTCACCACCCGCGGCTCTGGCCCAGGGGGCGCGGCCGGGACACTGGAGGGCGCCGCGGACCGCGCGGCTGGGGCTGGGGTCTCGGGGATTGCGGGGTCCGCCGCGGGGCCAGGAGTGGTCGGGACCGTCTCCGGGTTC

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.

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