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skill CX Codex GP ChatGPT official · OpenAI

ncbi-blast-skill — Codex skill: what it does, how to install

Submits searches to NCBI BLAST via the Common URL API, polls job status by RID, and formats compact summaries for nucleotide or protein sequences.

Install into Codex · Skills CLI (Vercel) All methods and platforms ↓ 
npx skills add openai/plugins --skill ncbi-blast-skill -a codex
Open on GitHub

What ncbi-blast-skill does

The skill handles sequence searches by calling scripts/ncbi_blast.py, which communicates with NCBI Blast.cgi. It supports blastn, blastp, blastx, tblastn, and tblastx. The script reads input JSON from stdin with target database, query FASTA, program, and email address. By default, it returns a compact summary capped at 5 top hits.

It enforces NCBI pacing rules: at least 10 seconds between requests and at least 60 seconds between polling attempts for the same RID. When full JSON2 or raw text alignments are required, the script writes them to a file. Running it requires Python with the requests package installed.

Install this skill if you work with NCBI sequence searches and want automated RID polling inside Codex. Without a need for NCBI BLAST lookups, this skill is unnecessary.

What it helps with

  • submit nucleotide or protein FASTA queries to NCBI BLAST
  • check job execution status using an assigned RID
  • retrieve top sequence hits with evalue and bit score metrics
  • save full JSON2 or text alignment results to a file

Example prompts for the agent

  • Run blastp for sequence MTEYK against swissprot with email [email protected]
  • Check the status of my NCBI BLAST job for this RID
  • Fetch results for RID and save raw JSON2 output to disk

How to install ncbi-blast-skill

1Skills CLI (Vercel)

npx skills add openai/plugins --skill ncbi-blast-skill -a codex

2Manually: put the files in place

.agents/skills/ncbi-blast-skill/SKILL.md

For all projects use ~/.agents/skills/

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Questions about ncbi-blast-skill

How do I install ncbi-blast-skill in Codex?

Run npx skills add openai/plugins --skill ncbi-blast-skill -a codex in your terminal.

What does ncbi-blast-skill do?

It submits FASTA sequences to NCBI BLAST, checks job progress by RID, and returns compact summaries of top hits.

What dependencies does the script require?

It requires Python with the requests library installed via python -m pip install requests, plus an email address for NCBI requests.

See also

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