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.

You will 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


This tutorial is a part of the tutorial group Alignment and comparison resources. You might find the other tutorials in the group interesting:

ClustalW2: Performs multiple sequence alignments

BLAST: Basic Local Alignment and Search Tool

FASTA: FASTA sequence algorithm

Entrez Gene: NCBI's Entrez tool for gene-centric information

DCODE: DCODE.org Comparative Genomics Developments, a collection of powerful comparative genomics tools

VISTA: Tools for Comparative Genomics

RefSeq: Provides molecular sequence records to help locate gene and protein data.


Algorithms and Analysis : This category contains various tools that may help perform analysis of different genomics data types. This may include sequence alignment, large-scale or complex queries, motif finding, or comparative assessments.

Nucleotides : Tools that are primarily used in the storage, retrieval, or exploration of nucleotide-based data. Some tools may also involve protein sequence information.


Simple primer design tools on the web: There are a lot of really complex bioinformatics tools and databases out there. But so often in training situations people ask us for something that solves a problem that is rather small and simple by ...


Recent BioMed Central research articles citing this resource

Dalman Kerstin et al., Overexpression of PaNAC03 , a stress induced NAC gene family transcription factor in Norway spruce leads to reduced flavonol biosynthesis and aberrant embryo development Biochemistry and physiology. BMC Plant Biology (2017) doi:10.1186/s12870-016-0952-8

Tian Qi et al., A novel NHS mutation causes Nance-Horan Syndrome in a Chinese family Clinical-Molecular Genetics and Cytogenetics. BMC Medical Genetics (2017) doi:10.1186/s12881-016-0360-9

Wingo S. Thomas et al., MPD: multiplex primer design for next-generation targeted sequencing Results and data. BMC Bioinformatics (2017) doi:10.1186/s12859-016-1453-3

Zhang Chen et al., Selection of reference genes from Shiraia bambusicola for RT-qPCR analysis under different culturing conditions. AMB Express (2017) doi:10.1186/s13568-016-0314-9

Zarek M. C. et al., Differential expression of genes related to gain and intake in the liver of beef cattle Genomics. BMC Research Notes (2017) doi:10.1186/s13104-016-2345-3