Online Research tools and Databases under We The Microbiologist

Here are some online tools for designing Primers for their respective experiments. Please use proper citation in your manuscript if you are using any of such tools mentioned here



For citation

Primer 3 (Version 4.0.0)

It is an online tool to design your primers for particular DNA sequence.

Primer3 - new capabilities and interfaces. Nucleic Acid Research


It is an online tool to design primers for Real Time PCR measurement of Eukaryotic expression.

DOI: 10.1186/gb-2004-5-5-p11

The PCR Suite

UCSC hosted online primer designing website

Contact at jeltje.van.baren at

Primer Blast

NCBI’s online primer designing tool and also used to check the specificity of the primers


Primer Quest Tool

IDT’s Primer designing tool for PCR and qPCR


PCR Designer for Restriction Analysis

Online PCR designing tool for Restriction analysis of sequence mutations

PubMed Link

Net Primer

Online Primer Analysis Software were primers are analyzed based on primer melting temperature and primer secondary structures


Web Primer

Simplest tool for designing primers for PCR or for sequencing offered by Stanford University