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Bioinformatics Advance Access published online on September 3, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti006
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received February 10, 2004
Revised July 5, 2004
Accepted August 4, 2004

Applications note

SNPbox, a modular software package for large scale primer design

Stefan Weckx 1, Peter De Rijk 1, Christine Van Broeckhoven 1, and Jurgen Del-Favero 1*

1 Department of Molecular Genetics, Bioinformatics Unit, Flanders Interuniversity Institute for Biotechnology, University of Antwerp, Antwerpen, Belgium

* To whom correspondence should be addressed. E-mail: jurgen.delfavero{at}ua.ac.be.


  Abstract

Summary: We developed a modular software package SNPbox that automates and standardizes the generation of PCR primers and is used in the strategy for constructing single nucleotide polymorphisms (SNPs) maps. In this strategy, the focus of primer design can be either on the validation of annotated public SNPs or on SNP discovery in exon regions or extended genomic regions, both by resequencing. SNPbox relies on Primer3 for the primer design and combines this program with other publicly available software tools such as BLAST, Spidey and RepeatMasker, and newly developed algorithms. Primer conditions are chosen such that PCR amplifications are uniform for each PCR amplicon facilitating the use of high-throughput genetic platforms. SNPbox can also be used for the design of primer sets for mutation analysis, STR marker genotyping and micro array oligo design. Of the 2500 primer sets we designed by SNPbox, 95% successfully amplified genomic DNA under uniform PCR conditions.

Availability: The software is available from the authors upon request.

Supplementary information: SNPbox_supplement


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