SNPbox: web-based high-throughput primer design with an eye for repetitive sequences

Stefan Weckx; Peter De Rijk; Wim Glassee; Christine Van Broeckhoven; Jurgen Del-Favero

doi:10.1007/978-1-59745-528-2_9

SNPbox: web-based high-throughput primer design with an eye for repetitive sequences

Methods Mol Biol. 2007:402:179-200. doi: 10.1007/978-1-59745-528-2_9.

Authors

Stefan Weckx¹, Peter De Rijk, Wim Glassee, Christine Van Broeckhoven, Jurgen Del-Favero

Affiliation

¹ Department of Molecular Genetics, Flanders Interuniversity Institute for Biotechnology (VIB), University of Antwerp, Belgium.

PMID: 17951796
DOI: 10.1007/978-1-59745-528-2_9

Abstract

In this omics era, researchers in biosciences need more than ever user-friendly, fast, and straightforward computational tools for high-throughput research. In this chapter, we present SNPbox and explain the general primer design strategy. We also show how the four modules, Exon, Single-Nucleotide Polymorphism (SNP), Saturation, and Exon + Saturation, exactly apply the primer design strategy, give clear guidance for users of the Web interface at http://www.SNPbox.org, and explain how pre-designed primers for Ensembl genes can be visualized and retrieved.

Publication types

Review

MeSH terms

DNA Primers* / chemistry
Exons
Internet*
Polymorphism, Single Nucleotide*
Repetitive Sequences, Nucleic Acid*
User-Computer Interface*

Substances

DNA Primers