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Bioinformatics Advance Access originally published online on April 8, 2004
Bioinformatics 2004 20(15):2399-2400; doi:10.1093/bioinformatics/bth257
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Bioinformatics 20(15) © Oxford University Press 2004; all rights reserved.

PUNS: transcriptomic- and genomic-in silico PCR for enhanced primer design

Paul C. Boutros * and Allan B. Okey

Department of Pharmacology, University of Toronto, Medical Sciences Building, 1 King's College Circle, Toronto, Ontario, M5S-1A8 Canada

Received on September 30, 2003; revised on February 3, 2004; accepted on February 4, 2004
Advance Access Publication April 8, 2004

Summary: We developed a CGI/Perl-based web server to perform in silico polymerase chain reaction (PCR) on PCR primer sequences. The PUNS (Primer-UniGene Selectivity) server simulates PCR reactions by running BLASTN analysis on user-entered primer pairs against both the transcriptome and the genome to assess primer specificity. PUNS is particularly suited for the identification of highly selective primers for quantitative microarray validation.

Availability: Both system access and source-code are freely available at http://okeylabimac.med.utoronto.ca/PUNS

Contact: Paul.Boutros{at}utoronto.ca

* To whom correspondence should be addressed.


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