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ncbi-sequence-fetch

Retrieve NCBI protein and nucleotide sequences via Entrez E-utilities with JSON output.

2.7k|283|Updated May 13, 2026
Search Tags:#rate limiting#bioinformatics#sequence retrieval#ncbi#cds translation#protein fasta#entrez e-utilities
One-click install
npx skills add https://github.com/google-deepmind/science-skills --skill ncbi-sequence-fetch
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ncbi-sequence-fetch
Source: https://github.com/google-deepmind/science-skills/tree/main/skills/ncbi_sequence_fetch
Command: npx skills add https://github.com/google-deepmind/science-skills --skill ncbi-sequence-fetch

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires python-dotenv, scienceskillscommon, and includes scripts (resource) components.

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.

Frequently Asked Questions about ncbi-sequence-fetch

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I fetch protein and nucleotide sequences from NCBI using Entrez E-utilities?▼

You can fetch protein and nucleotide sequences from NCBI using Entrez E-utilities by defining operations in YAML helper scripts, which use efetch and esearch to return structured JSON results for your queries.

Can I retrieve a protein sequence from a nucleotide CDS record?▼

Yes, you can translate CDS or nucleotide records into protein sequences using pre-translated CDS extraction, GenBank XML CDS parsing, or 6-frame ORF translation workflows within the retrieval process.

Does retrieving sequences from NCBI support searches by locus tag or PubMed ID?▼

Retrieving NCBI sequences supports flexible search entry points including gene and organism names, locus tags, PubMed-linked proteins, patent-related protein extraction, and accession lookups.

How do I avoid NCBI rate limiting when fetching multiple sequences in a workflow?▼

To avoid NCBI rate limiting, the sequence retrieval process gracefully throttles requests at 3 per second, or 10 per second if you configure an optional NCBI_API_KEY with controlled credential handling.

What is the best way to get structured JSON outputs for NCBI FASTA sequences?▼

The best way to get structured JSON outputs for NCBI FASTA sequences is to use YAML-defined operations via helper scripts that query Entrez E-utilities and format the retrieved protein or nucleotide data into JSON.

Do I need to paste my NCBI API key directly into the chat to increase request limits?▼

No, you do not need to paste your NCBI API key into the chat, as the sequence retrieval process uses controlled credential handling to securely manage optional rate-limit increases via environment configuration.

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