JCVI Primer Designer


Polymerase chain reaction (PCR) is used in directed sequencing for the discovery of novel polymorphisms.  As the first step in PCR directed sequencing, effective PCR primer design is crucial for obtaining high-quality sequence data for target regions.  Since current computational primer design tools are not fully tuned with stable underlying laboratory protocols, researchers may still be forced to iteratively optimize protocols for failed amplifications after the primers have been ordered.  Furthermore, potentially identifiable factors which contribute to PCR failures have yet to be elucidated.  This inefficient approach to primer design is further intensified in a high-throughput laboratory, where hundreds of genes may be targeted in one experiment.


We have developed a fully integrated computational PCR primer design pipeline that plays a key role in our high-throughput directed sequencing pipeline.  Investigators may specify target regions defined through a rich set of descriptors, such as Ensembl accessions and arbitrary genomic coordinates.  Primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the specified target regions.  As part of the tiling process, primer pairs are computationally screened to meet the criteria for success with one of two PCR amplification protocols.  In the process of improving our sequencing success rate, which currently exceeds 95% for exons, we have discovered novel and accurate computational methods capable of identifying primers that may lead to PCR failures. 


The high-throughput PCR primer design pipeline has been very successful in providing the basis for high-quality directed sequencing results and for minimizing costs associated with labor and reprocessing.  The modular architecture of the primer design software has made it possible to readily integrate additional primer critique tests based on iterative feedback from the laboratory.  As a result, the primer design software, coupled with the laboratory protocols, serves as a powerful tool for low and high-throughput primer design to enable successful directed sequencing.



                   How to acquire the JCVI Primer Design software.



                   How to install the JCVI Primer Design Software.


How to run through a few key workflows.


            Frequently Asked Questions

                   Answers to questions posed by users that might be asked again.


            Download Publication

                   Get a copy of the JCVI Primer Design Manuscript


Kelvin Li, Anushka Brownley, Timothy B Stockwell, Karen Beeson, Tina C McIntosh, Dana Busam, Steve Ferriera, Sean Murphy, Samuel Levy, “Novel computational methods for increasing PCR primer design effectiveness in directed sequencing”, BMC Bioinformatics 2008, 9:191 (11 April 2008)