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ncbi-sequence-fetch

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Retrieve protein and nucleotide sequences from NCBI databases using E-utilities. Supports direct accession lookup, CDS translation, gene+organism search, locus lookup, PubMed-linked sequences, patent protein extraction, and organism+length fallback search. Use when you need to fetch biological sequences by accession, gene name, locus tag, PubMed ID, or patent number.

skills/ncbi_sequence_fetch/SKILL.md

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Oct 23, 2026
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Apache-2.0

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# NCBI Sequence Fetch

## Prerequisites

1.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
    `uv` is installed and on PATH.
2.  **User Notification**: If .licenses/ncbi_sequence_fetch_LICENSE.txt does not
    already exist in the workspace root directory then (1) prominently notify
    the user to check the terms at https://www.ncbi.nlm.nih.gov/ and
    https://www.ncbi.nlm.nih.gov/home/about/policies/, then (2) create the file
    recording the notification text and timestamp.
3.  **`.env` file**: Make sure the `.env` file exists in your home directory.
    Create one if it does not exist.
4.  **`NCBI_API_KEY`** (optional): Raises the NCBI rate limit from 3 to 10