Is there a software that can suggest which primer combination should go in a multiplex PCR?

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Kenneth Day

I often use this web-based tool to help with this problem you are describing and then divide up my primer groups.

https://www.lifetechnologies.com/us/en/home/brands/thermo-scientific/molecular-biology/molecular-biology-learning-center/molecular-biology-resource-library/thermo-scientific-web-tools/multiple-primer-analyzer.html

I also found this tool helpful when trying to quickly design multiplexed primer sets across exons in the same gene.

http://pcrtiler.alaingervais.org:8080/PCRTiler/

Raewyn Billings

I have used Mprimer, it worked well for one set of primers, around 40 primer pairs.

http://biocompute.bmi.ac.cn/CZlab/mprimer/

Hosseinali Abdi

Hi Natascha,

A program for reliable multiplex PCR primer design

http://biocompute.bmi.ac.cn/MPprimer/run_example.html

Silas S. Brown

Hi Natascha, I realise your question is now a year old and you must have sorted it out by now, but perhaps I should post this here in case others want it.

http://ssb22.user.srcf.net/pooler/

Gennady Khvorykh

I also advise the Primer Pooler program mentioned above. It checks specificity, counts thermodynamic values (dG), and swaps primers to minimize the possible formation of dimers. http://people.ds.cam.ac.uk/ssb22/pooler/

Natascha Techen

Thank you for all your responses. Typing in

http://people.ds.cam.ac.uk/ssb22/pooler/

won't give me access to the website. Says is 'Forbidden'. Maybe not accessible from the US?

The link http://people.ds.cam.ac.uk/ssb22/pooler/ became forbidden for me too. This is the link to the article describing PrimerPooler https://academic.oup.com/biomethods/article/2/1/bpx006/3760164

Silas S.Brown answered above is the developer of the program. Probably he could be of help.

Sorry about the Forbidden. It was a server error. http://ssb22.user.srcf.net/pooler/ works. The previous server has been permanently shut down by the university.

Kishore Bhat

thanks for the information. I am trying to design primers for multiplex PCR of bacterial subspecies. will try this software and get back to you with my results.