PCR Primer Design

Our work on PCR primer design is based around the software library PD5. This is  a flexible library of open source C++ code for a wide variety of primer design applications. We are in the process of submitting an article describing PD5, and in the meantime, further information and examples of applications can be found at the PD5 source code site.

We also have a simple web interface to PD5 for basic primer design at PD5web

Some of the primer sets that have been designed using PD5 include:

  • S. pombe gene deletion confirmation primers. These are primers that flank each ORF in S. pombe and allow us to confirm the presence or absence of the ORF. Primers are available for 5064 ORFS in pombConf_v1.csv and a further 63 ORFs designed by additionally relaxing the check for non-specific binding in pombConf_noNSBcheck_v1.csv.
  • Primers for Precise Deletion of genes from several organisms.

This work was funded by BBSRC grant BB/G024782/1, and the proposal can be seen on figshare.