Amplify · experimental
PCR Simulation
Check a primer pair against a template and get the product it would actually produce, or find that it produces none. Fusion PCR and multiplex screening run on the same annealing engine, each with its own tool.
Real sequences (GenBank plasmid, FASTA, and a protein family) for the Primer Designer
What it does
- 01Primer annealing detection on both strands, reporting the product or the reason there is none
- 02Amplicon construction with annotations carried from the template
- 03Nearest-neighbour thermodynamics per primer, including 3-prime end free energy
- 04Products opened as sequences, or passed to an assembly tool
What it runs on
Amplification runs on the pydna port, golden-tested byte for byte against pydna. The panel runs on @ports/fusion, @ports/gel, @ports/multiplex, @ports/pcr, @ports/primer.
Everything runs client-side. Files are parsed in the browser and projects are saved on this machine, so an unpublished sequence is never uploaded.
Questions
- What happens when my primers do not amplify?
- The tool says so and states why, rather than returning an empty table. A pair that does not anneal as an amplifying pair is reported as such.
- Can a PCR product feed straight into an assembly?
- Yes. A product can be opened as a sequence in the project, which is what the Gibson and Golden Gate tools read their fragments from.
Also searched as
PCR simulator online · in silico PCR · virtual PCR product · amplicon prediction tool · primer pair product check · predict pcr product from primers · UCSC in-silico PCR alternative · predict amplicon size from primers · check primers before ordering · free PCR simulator · will these primers work