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

Boeglin Martin et al., Reduced expression of AtNUP62 nucleoporin gene affects auxin response in Arabidopsis Development and cell biology. BMC Plant Biology (2016) doi:10.1186/s12870-015-0695-y

Rodrigues B. Thais et al., Carbon dioxide receptor genes and their expression profile in Diabrotica virgifera virgifera Molecular Biology. BMC Research Notes (2016) doi:10.1186/s13104-015-1794-4

Song Li et al., Genome-wide transcriptome analysis of soybean primary root under varying water-deficit conditions Plant genomics. BMC Genomics (2016) doi:10.1186/s12864-016-2378-y

Kwenda Stanford et al., Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen Pectobacterium atrosepticum Prokaryote microbial genomics. BMC Genomics (2016) doi:10.1186/s12864-016-2376-0

Banani Houda et al., Genome sequencing and secondary metabolism of the postharvest pathogen Penicillium griseofulvum Eukaryote microbial genomics. BMC Genomics (2016) doi:10.1186/s12864-015-2347-x