The PCR Suite

Welcome to the new location of PCR Suite: a collection of programs that interact with the Whitehead's Primer3 program.

Please note: This program is hosted by UC Santa Cruz but is not maintained by them. The author can be reached at jeltje.van.baren at

The original Primer3 program designs primersets for one sequence and it allows you to change almost every parameter. The PCR Suite has more stringent settings (to allow more working primersets) and a smaller range of parameters (because you won't change most of them anyway).
The suite consists of four programs:

Overlapping_Primers is for creating multiple overlapping PCR products in one sequence.
Genomic_Primers designs primers around exons in genomic sequence. All you need is a GenBank file containing your gene.
SNP_Primers designs primers around every SNP in a GenBank file.
cDNA_Primers designs primers around open reading frames. Simply upload a GenBank file containing your genes.

Click here if you want to know how to obtain GenBank files with genomic sequence.
Click here if you want to know how to obtain GenBank files with cDNA sequences.

If you want to know more about using the PCR Suite, if something doesn't work, or if you have comments or suggestions, please email the author.

If these programs have been useful to you, please cite:
The PCR Suite M.J. van Baren and P. Heutink. Bioinformatics. 2004 Mar 1;20:591-3

This software is based on the Primer3 program developed by the Whitehead institute. The Primer3 core program used by PCR Suite was developed by the Whitehead Institute and used "as is". See the copyright notice and disclaimer for PCR Suite and the Whitehead's Primer3
The source code for PCR Suite is available here.
A detailed description of how PCR Suite interacts with Primer3 can be found here.