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Pick primers from a DNA sequence.

Tutorial and training materials by OpenHelix

Learn to use Primer3, a handy tool for primer design. Oligonucleotide primers are widely used in molecular biology applications, and Primer3 offers many ways to identify appropriate oligos for your research. Simple, quick primer designs are possible--as well as options for more detailed primer characteristics which are available to fine tune your primer choices.
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You'll learn:

  • simple, basic primer selection
  • to access more detailed primer design features, and check for mis-priming in your template
  • to find the Primer3 source code, which can be used by programmers for many applications


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Recent BioMed Central research articles citing this resource

Zhou Xiaojing et al., Construction of a SNP-based genetic linkage map in cultivated peanut based on large scale marker development using next-generation double-digest restriction-site-associated DNA sequencing (ddRADseq) Plant genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-351

Sutherland JG Ben et al., Comparative transcriptomics of Atlantic Salmo salar , chum Oncorhynchus keta and pink salmon O. gorbuscha during infections with salmon lice Lepeophtheirus salmonis Comparative and evolutionary genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-200

Ingham B Aaron et al., RNF14 is a regulator of mitochondrial and immune function in muscle Empirical systems biology. BMC Systems Biology (2014) doi:10.1186/1752-0509-8-10

Busk K Peter et al., A tool for design of primers for microRNA-specific quantitative RT-qPCR Transcriptome analysis. BMC Bioinformatics (2014) doi:10.1186/1471-2105-15-29

Renault Tristan et al., Genotyping of a microsatellite locus to differentiate clinical Ostreid herpesvirus 1 specimens. Veterinary Research (2014) doi:10.1186/1297-9716-45-3

More about the resource:

The Primer3 tool, which is used for the design of primers (oligos) for molecular biology research, was developed by Steve Rozen and Helen Skaletsky at MIT. This software helps researchers to generate PCR primers, sequencing primers, hybridization oligos--or for your short oligonucleotide fragment needs of almost any sort. This tool is freely available to the public, and can be found not only at the MIT Whitehead Institute website, but installed locally in many other institutions and companies as well. All of these Primer3 sites include software developed by the Whitehead Institute for Biomedical Research.


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