Tool:PrimerServer: a high-throughput primer design and specificity-checking platform
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4.2 years ago
bill-zt ▴ 50

We are happy to release PrimerServer, a high-throughput primer design and specificity-checking platform.

Project Page

Demo Server


Zhu T, Liang CZ, Meng ZG, Li YY, Wu YY, Guo SD* and Zhang R* (2017). PrimerServer: a high-throughput primer design and specificity-checking platform. bioRxiv 181941 (


Nowdays, it is easy to design one primer pair specific to the whole genome in a modal organism. Many programs such as NCBI primer-BLAST can conduct this well. However, what if you want to design multiple primer pairs that are specific to a custom genome? Besides, how to do this for both normal users (GUI needed) and bioinformatics users? (CLI needed, for large amount of sites). Here are several issues raised in BioStar:

We anticipate that PrimerServer can satisfy all of this.

  • Very easy to install. Only uses three tools: Primer3, Samtools and NCBI BLAST+. No other special modules or plugins needed.
  • Very nice GUI: Running progress bar, primer gragh, virtual gel electrophoresis, parameters and results storage
  • Very fast CLI: multiple threaded, ~0.4s per site for designing primers for >10,000 sites
  • High accuracy

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For feedbacks, please use the GitHub tracking issues, or just send an email to

Thank you!

primer blast PCR Tool • 2.5k views

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