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Bioinformatics Vol. 18 no. 11 2002
Pages 1538-1539
© 2002 Oxford University Press

Applications Note

AcePrimer: automation of PCR primer design based on gene structure

Sheldon J. McKay and Steven J.M. Jones *

Genome Sciences Centre, British Columbia Cancer Agency, 600 W 10th Avenue, Vancouver, BC, Canada V5Z 4E6

Received on December 4, 2001 ; revised on February 12, 2002 and April 22, 2002 ; accepted on April 30, 2002

Summary: AcePrimer is an internet-accessed application based on CGI/Perl programming that designs PCR primers to search for deletion alleles in Caenorhabditis elegans gene knockout experiments and uses electronic PCR to search the entire genomic DNA sequence for potential false priming or multiple PCR amplification targets. Features such as the ability to target specific exons with the ‘poison primer’ approach and evaluation of primers with electronic PCR provide a flexible, web-based approach to design effective primers whilst minimizing the need for empirical optimization of PCR experiments.

Availability: Web access to this program is provided at http://elegans.bcgsc.bc.ca/gko/aceprimer.shtml.

* To whom correspondence should be addressed.


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