ncbi-sequence-fetch
OfficialFetch protein & nucleotide sequences from NCBI
Education & Research#rate limiting#bioinformatics#sequence retrieval#ncbi#cds translation#protein fasta#entrez e-utilities
Authorgoogle-deepmind
Version1.0.0
Installs0
System Documentation
What problem does it solve?
It eliminates the manual, error-prone work of finding, translating, and downloading biological sequences from NCBI when you only have accessions, gene names, locus tags, PubMed IDs, or patent numbers.
Core Features & Use Cases
- NCBI E-utilities sequence retrieval: Pulls protein and nucleotide FASTA from NCBI using efetch/esearch and returns structured JSON results.
- CDS translation workflows: Converts CDS or nucleotide records into protein sequences via pre-translated CDS, GenBank XML CDS extraction, or 6-frame ORF translation.
- Flexible search entry points: Supports gene+organism, locus tag, PubMed-linked proteins, patent protein extraction, and a last-resort organism+length lookup.
- Rate-limit and API-key support: Uses graceful throttling at 3 req/s (10 req/s with NCBI_API_KEY) and avoids asking users to paste secrets into chat.
Quick Start
Use the skill to fetch the protein FASTA for accession XP_022033624 by asking for a JSON output file location.
Dependency Matrix
Required Modules
python-dotenvscienceskillscommon
Components
scripts
💻 Claude Code Installation
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Please help me install this Skill: Name: ncbi-sequence-fetch Download link: https://github.com/google-deepmind/science-skills/archive/main.zip#ncbi-sequence-fetch Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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