skills.rest
LeonChaoX
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uniprot-database

Search UniProt proteins and retrieve sequences via REST endpoints.

783|65|Updated Feb 27, 2026
Search Tags:#batch processing#rest api#uniprot#protein search#id mapping#fasta retrieval
One-click install
npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill uniprot-database-leonchaox
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: uniprot-database
Source: https://github.com/LeonChaoX/qinyan-academic-skills/tree/main/skills/08-%E8%9B%8B%E7%99%BD%E8%B4%A8%E5%B7%A5%E7%A8%8B%E4%B8%8E%E7%BB%93%E6%9E%84%E7%94%9F%E7%89%A9%E5%AD%A6/uniprot-database
Command: npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill uniprot-database-leonchaox

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill eliminates the manual effort of locating, downloading, and mapping protein information by providing a direct, programmatic UniProt REST API workflow for researchers.

Core Features & Use Cases

  • Protein search and retrieval: Find proteins by name, gene, accession, organism, or GO term, then fetch entries in formats such as JSON/TSV/FASTA.
  • ID mapping across bioinformatics resources: Convert identifiers between UniProtKB and external databases (e.g., Ensembl, RefSeq, PDB, AlphaFoldDB) using UniProt’s idmapping service.
  • Efficient large dataset handling: Stream large query results to avoid pagination bottlenecks and reduce operational overhead.

Use case: You have a list of human genes and need their UniProt accessions plus FASTA sequences for downstream analysis; you can search, map, and retrieve sequences with consistent API calls.

Quick Start

Ask for protein FASTA sequences from UniProt for a query like insulin AND organism_name:"Homo sapiens" and return the results in FASTA format using UniProt’s REST search endpoint.

Frequently Asked Questions about uniprot-database

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

FAQPage Schema
How do I retrieve protein FASTA sequences from UniProt in bulk?▼

You can retrieve protein FASTA sequences in bulk via the UniProt REST search endpoint by stream processing large result sets, which avoids pagination bottlenecks and handles downstream sequence acquisition.

How does ID mapping work for converting Ensembl or RefSeq identifiers to UniProt accessions?▼

ID mapping converts identifiers between UniProtKB and external databases like Ensembl, RefSeq, PDB, and AlphaFoldDB by submitting an idmapping job and retrieving status updates and results for cross-database workflows.

What is the best way to search UniProt for proteins by organism or GO term?▼

The best way to search UniProt for proteins is using the REST API to query by name, gene, accession, organism, or GO term, then fetch entries in formats like JSON, TSV, or FASTA for annotation workflows.

Does the UniProt REST API support streaming for large protein datasets?▼

Yes, the UniProt REST API supports streaming for large result sets, allowing you to process extensive protein search results efficiently with optional field selection and robust batching limits.

What are the limitations of batch processing UniProt protein search results?▼

Batch processing limitations for UniProt protein search include operational overhead from pagination bottlenecks and the need for robust batching limits to manage large query result sets effectively.

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