I am trying to write a research paper on PRIMER-BLAST. I have read something about it on


but still, it is not enough. So can you please tell me more about it or suggest some resources.

  • 1
    $\begingroup$ I'm not sure if it's just the language barrier and you actually meant something else, but...if you are unaware of basic tools for finding scientific papers (such as Google Scholar, Web of Science), and of good practices (such as following up citations of interest), then perhaps you shouldn't be writing a research paper just yet? $\endgroup$
    – Laura
    Apr 27, 2020 at 8:07

1 Answer 1


I would start at the Primer3 website here.

Once you understand all the variables on the website via the manual here and the associated publications Koressaar et al (2007) and Untergasser et al (2012) you will understand the gist of the algorithm used in primer design. This gives you optimised primers for a single strand of DNA/RNA

Primer-Blast looks in addition at maximising sequence conservation within an alignment of different sequences. The alignment is created using a Blast (I think its Mega-Blast. Thus Primer-Blast looks at one more parameter accounting for mutation heterogeneity which might be encountered in the PCR/RT-PCR and the number of primers it recommends is therefore reduced over say PRimer3.

Prove it for yourself take a given sequence and run it through Primer3 and then Primer-Blast and assess the differences and similarities.


Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG (2012) Primer3 - new capabilities and interfaces. Nucleic Acids Research 40(15):e115

Koressaar T, Remm M (2007) Enhancements and modifications of primer design program Primer3 Bioinformatics 23(10):1289-91


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