Ncbi Sequence Fetch
Retrieve protein and nucleotide sequences from NCBI databases using E-utilities.
Install
npx skills add google-deepmind/science-skills --skill ncbi-sequence-fetch -g -a claude-code -y- Repository
- google-deepmind/science-skills3.4k
- Category
- Engineering
- Updated
- 12d ago
- License
- Apache-2.0
- Context cost
- Mediumabout 2,146 tokens
- Runs scripts
- Yes, review before use
What it does
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.
NCBI Sequence Fetch
Prerequisites
uv: Read theuvskill and follow its Setup instructions to ensureuvis installed and on PATH.- 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.
.envfile: Make sure the.envfile exists in your home directory. Create one if it does not exist.NCBI_API_KEY(optional): Raises the NCBI rate limit from 3 to 10 requests/second. The skill works without it, but a key is recommended if the user plans many queries or encounters a 429 error. You can register for a key for free at https://www.ncbi.nlm.nih.gov/account/settings/. You MUST use the safe credentials protocol in thecredentialsskill to check for and request this key if this skill looks relevant to the user's request.
Core Rules
- Use the Wrapper: ALWAYS execute the provided helper scripts to query the database rather than accessing the database directly. The scripts automatically enforce the required rate limit gracefully.
- API Key Support: If the user provides an
NCBI_API_KEYin their environment, the query speed limits are automatically increased significantly. - Notification: If this skill is used, ensure this is mentioned in the output.
Overview
Wraps NCBI's Entrez E-utilities (efetch, esearch, elink, esummary) for retrieving protein and nucleotide sequences. Provides 10 subcommands covering the full range of sequence retrieval workflows:
