Automated Primer Designer

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Installation Instructions

Primer Designer Introduction

This is a perl-based primer design script. It allows the user to input a series of SNP locations and outputs a file with correlating primer sequences.

To use the script, save your SNPs to a textfile named TestSNPs.txt like this:

  • chr2 3894843
  • chr6 837594
  • chrM 5938

and save the file in the Primer-Designer directory.

Then, just run the perl script:


The script will then ask you what genome you would like SNPs from. For example, enter HG19 for the most current build of the human genome. If it doesn't have it already, the script will download the genome, extract the sequences flanking your SNPs, run them through primer3 and output them to a new file.

The primer sequences are references against the RepBase mispriming library while running in primer3.

When finished, the script will save a new file called final_primers.fa in the Primer-Designer directory. It will contain fasta-formatted primer sequences with your SNP IDs.

While this script will theoretically work for any eukaryotic genome, bear in mind that the script runs completely locally - so will download and decompress whatever genome you request onto your machine. We are currently working on a more lightweight method - if you would like to be alerted when we have it, feel free to email us.

The code is relatively simple and well-commented, so feel free to tinker.

This script is written by Russell Durrett and Joseph Steinberger in the Mason Lab. Email your questions to Russell at

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