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PCR primer designer
Give it a target sequence. Get primer pairs checked for temperature, off-target matches and clear coordinates.
PCR primer designer is a free AI skill for the job "Research a topic properly". Give the instructions to an AI assistant that supports the required files and tools, then review its output.
Free · No account · MIT licence · Made by K-Dense · Level: advanced
Made by K-Dense. See the original on GitHub; we copied it as it is, with its licence.
What it does
Primer pairs you can trust, with the proof behind them. Give a target sequence and get candidate primers with melting temperature, secondary structure, off-target matches and exact product coordinates checked, not just a good-looking score. The skill first pins down the assay: template, chemistry, reference genome and intended products. It then designs primers with Primer3, calculates thermodynamics with supplied tools, and screens every possible product across your search scope. It handles exon junctions, tailed cloning primers, multiplex panels and checking pairs you already own. Degenerate, bisulfite and probe assays are flagged as needing a special route. Local tools and a reference database are needed.
You give it
- Target sequence or coordinates
- Species and reference genome
- Assay type and chemistry
- Existing primers (optional)
- Product size range
You get
- Ranked primer pairs in 5 to 3 order
- Melting temperature and structure checks
- Off-target product screen
- Exact product coordinates and sequence
Use it when
- You need a primer pair for a gene and want to know it will not amplify anything else.
- You have existing primers and want them checked against a genome.
- You are designing an RT-qPCR assay that spans an exon junction.
- You are adding cloning tails and need the final product rebuilt.
How to use it
- Add it to your AI once: download it and add the folder to Claude, ChatGPT or Codex as a skill.
- Ask for the job in your own words. Your AI opens the skill when it fits.
- It works best when your AI can run code.