Bio-chat: Hardcore Primer Designer

v5.1.0

Designs high-specificity RT-qPCR primers and probes with homology mapping, high-GC optimization, TaqMan/SYBR support, and off-target specificity checks.

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LicenseMIT-0 · Free to use, modify, and redistribute. No attribution required.
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Purpose & Capability
The name/description announce primer/probe design with homology mapping, high-GC Tm calculation, TaqMan/SYBR support and off-target checks — and the included Python implements those features (SantaLucia NN Tm calc, homology-based junction mapping, off-target substring checks, probe selection). The required resources (no credentials, only NCBI network access) are consistent with designing assays from NCBI accessions.
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Instruction Scope
SKILL.md states you can provide either an NCBI accession OR a local FASTA, but the script only accepts accessions and always calls NCBI efetch (get_transcript). Supplying a local FASTA path will not be handled as advertised. The runtime will perform outbound HTTP requests to NCBI eutils (expected for this purpose) and prints sequence/annotation fetch attempts; it does not send data to any third-party endpoints beyond NCBI.
Install Mechanism
There is no install spec; the package is instruction-only with one Python script and requirements.txt (requests). That is low-risk, but users must ensure the runtime environment has the 'requests' library or install it themselves.
Credentials
The skill requests no environment variables, credentials, or special config paths. Its only external interaction is unauthenticated HTTP GETs to NCBI eutils, which is proportionate to fetching sequences/annotations.
Persistence & Privilege
The skill is user-invocable and not always-enabled. It does not request persistent privileges and does not attempt to modify other skills or system configuration.
Assessment
This skill appears to do what it says: it fetches sequences from NCBI and runs primer/probe design locally without requesting secrets. Before installing/using: (1) Note the SKILL.md claim that local FASTA input is supported is inaccurate — the current script expects NCBI accessions and will try to fetch from NCBI; if you need local FASTA support, modify the script or pass sequences another way. (2) The homology/junction mapping uses simple substring searches and minimal GenBank parsing — this can produce incorrect junction mappings for real-world, noisy sequences; validate outputs manually before ordering primers. (3) The script performs outbound network requests to NCBI (no authentication) — if your environment disallows network egress, run it locally with vetted inputs. (4) There are no hidden endpoints or credential exfiltration, but because this is a biological assay tool, ensure you have appropriate institutional approvals and biosafety review before designing assays for regulated or pathogenic organisms. Finally, review and test the code on non-sensitive examples, and ensure 'requests' is installed in the Python environment.

Like a lobster shell, security has layers — review code before you run it.

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License

MIT-0
Free to use, modify, and redistribute. No attribution required.

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