primer-design SKILL.md skillA
primer-design from k-dense-ai/scientific-agent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add k-dense-ai/scientific-agent-skills/primer-design@v1.1Pins v1.1 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- k-dense-ai/scientific-agent-skills
- Path
skills/primer-design/SKILL.md- Versions recorded
- 2
- Latest version
- v1.1, committed Oct 1, 2026
- First version recorded
- Sep 30, 2026
- Size
- 16,361 bytes
- Repository stars
- 56,497
- License
- MIT
Designs and audits PCR and RT-qPCR primers with Primer3, explicit thermodynamic conditions, reference-based off-target amplification searches, and traceable sequence coordinates. Use for designing primer pairs, checking existing primers, exon-junction or isoform-specific assays, variant masking, cloning tails, multiplex compatibility, and interpreting Primer-BLAST results. Includes bounded local in-silico PCR and BLAST screening; distinguishes computational candidates from experimentally…
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# Primer design and specificity Produce candidate oligos in 5-prime-to-3-prime orientation, with the exact template, chemistry, intended products, and search scope behind each conclusion. Calculate sequence-dependent quantities with the supplied tools. A familiar gene name, good Primer3 penalty, or a single BLAST alignment cannot establish primer specificity. ## Choose the workflow | Request | Start here | | --- | --- | | New genomic PCR or RT-qPCR pair | Define the assay and reference; design; assess thermodynamics; screen products. | | Check an existing pair | Prepare pair TSV; assess both full oligos and annealing cores; screen with explicit intended coordinates. | | Exon junction, transcript isoform, allele discrimination | Read [design-workflows.md](references/design-workflows.md); supply sequence annotation before imposing constraints. | | Cloning/adaptor-tailed primers | Design annealing cores, append declared 5-prime tails, reassess full oligos, reconstruct the final product. | | Multiplex panel | Enable `--multiplex` in both thermodynamics and specificity tools to assess oligo interactions and cross-pair products. | …
Read the whole file at its exact version.
How to install
mdr add k-dense-ai/scientific-agent-skills/primer-design@sha256:ea8bed0aa340a5f6The line at the top of this page pins the label v1.1, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_b2q3mfrhg35fppml)
2 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 2 versions of this file, between Sep 30, 2026 and Oct 1, 2026, more than one a day.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| v1.1 latest | 2026-10-01 | a92663a | 16,361 B | A | view · diff |
| v1.0 | 2026-09-30 | 51f621c | 15,896 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (16361 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
k-dense-ai/scientific-agent-skills · 56,497 stars · license MIT · pushed 2026-11-02 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_b2q3mfrhg35fppml GET https://markdownregistry.com/api/v1/resolve?ref=k-dense-ai/scientific-agent-skills/primer-design GET https://markdownregistry.com/api/v1/blob/ea8bed0aa340a5f6538c206bb3d9fe503da6759e68a944a2bce564fa115d25e4
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.