Skip Navigation


Bioinformatics Advance Access originally published online on September 3, 2004
Bioinformatics 2005 21(3):385-387; doi:10.1093/bioinformatics/bti006
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
21/3/385    most recent
bti006v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (7)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Weckx, S.
Right arrow Articles by Del-Favero, J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Weckx, S.
Right arrow Articles by Del-Favero, J.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics vol. 21 issue 3 © Oxford University Press 2005; all rights reserved.

SNPbox: a modular software package for large-scale primer design

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

Department of Molecular Genetics (VIB8), Bioinformatics Unit, Flanders Interuniversity Institute for Biotechnology, University of Antwerp Universiteitsplein 1, B-2610 Antwerpen, Belgium

*To whom correspondence should be addressed.

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 the 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 were 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 microarray oligo design. Of the 2500 primer sets designed by SNPbox, 95% successfully amplified genomic DNA under uniform PCR conditions.

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

Contact: jurgen.delfavero{at}ua.ac.be

Supplementary information: SNPbox_supplement.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
F. Zhang and Z. Zhao
SNPNB: analyzing neighboring-nucleotide biases on single nucleotide polymorphisms (SNPs)
Bioinformatics, May 15, 2005; 21(10): 2517 - 2519.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
S. Weckx, J. Del-Favero, R. Rademakers, L. Claes, M. Cruts, P. De Jonghe, C. Van Broeckhoven, and P. De Rijk
novoSNP, a novel computational tool for sequence variation discovery
Genome Res., March 1, 2005; 15(3): 436 - 442.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.