Free primer design programs

Article Navigation. Close mobile search navigation Article Navigation. Volume Article Contents Abstract. Classification and review of free PCR primer design software.

Jingwen Guo , Jingwen Guo. Department of Computer Science. Oxford Academic. Google Scholar. David Starr. Department of Pathology, Saint Louis University. Huazhang Guo. To whom correspondence should be addressed. Revision received:. A word to the wise: check on the primer without any added restriction sites for cloning before ordering your primer.

After the sequence is submitted and analyzed you can also sort results by primer length, melting temperature, and more. My favorite part of using PrimerBlast is that it provides a visual interface including where the primers will bind on the template. BatchPrimer3: This is a great tool for performing a more high-throughput primer design. BatchPrimer3 is based on Primer3 and can design a wide variety of primers.

Results are provided as an HTML with color-coded alignment visualization, and can be downloaded in tab-delimited form. HYDEN is a command-line based downloadable program that designs primers cover many input sequences. A quick word to the wise before plugging in all your favorite templates: do ensure you have a detailed understanding of how PCR works and your specific application prior to designing and ordering primers.

It is nice and simple to use with minimal primer parameters to set. You have more flexibility, compared to their Real-time PCR TaqMan Primer Design interface, in setting a plethora of primer parameters by using their advanced tab.

AutoPrime is specific for qPCR applications that want to measure eukaryotic gene expression. The platform is based on Primer3, and puts a lot of emphasis on amplifying cDNA, therefore only primers spanning exon-exon boundaries and those separated by an intron will be generated. This will allow for more efficient primer binding and ultimately improve your PCR results.

BatchPrimer3 is yet another Primer3-based primer design software freely available online. There is a huge amount of primer subtypes to design including, generic PCR primers. An intermediate selection of primer parameters are also there to tweak. All that is required is a target sequence, which is copied and pasted into the program, then you have the option to tweak the design parameters.

The output also includes a suggested annealing temperature to use for each primer pair. Do you have any free PCR primer design software suggestions to add to the list?

Leave a comment below with your preferred choice and I will be sure to update the list. Hi Thank You Steven for the great help. I need to know if any of these softwares can help me design multiplex pcr primer sets I need something to help me analyse Self Complementary structures. Hi Nima Many thanks for your comment. For multiplex primer design tools that are free, your choices are rather limited.

I did see a recent one called oli2go.