uniprot-database

Query UniProt REST API for protein search, FASTA retrieval, and ID mapping.

1|Updated Mar 11, 2026

Search Tags:#bioinformatics #sequence #mapping #rest-api #protein #uniprot

Ready to run

npx skills add https://github.com/SciMate-AI/scicli --skill uniprot-database-scimate-ai

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: uniprot-database
Source: https://github.com/SciMate-AI/scicli/tree/main/internal/skills/bundled/claude-scientific-skills/skills/uniprot-database
Command: npx skills add https://github.com/SciMate-AI/scicli --skill uniprot-database-scimate-ai

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Direct programmatic access to UniProt REST API enabling fast protein search, sequence retrieval, and cross-database ID mapping without manual browsing.

Core Features & Use Cases

Searching proteins by name, gene, accession, or organism
Retrieving sequences in FASTA or other supported formats
Mapping identifiers across databases (Swiss-Prot/TrEMBL, Ensembl, RefSeq, PDB)
Batch retrieval and streaming of large result sets for scalable analyses

Quick Start

Query a protein by accession via the UniProt REST API to retrieve its JSON entry.

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 sequences in FASTA format from UniProt programmatically?▼

The UniProt REST API supports cross-database ID mapping to translate identifiers across Swiss-Prot, TrEMBL, Ensembl, RefSeq, and PDB. This Skill automates mapping workflows for scalable batch operations.

Can I stream large datasets from UniProt for batch protein search?▼

You can search proteins by querying name, gene, accession, or organism through the UniProt REST API search endpoint. Optional fields and format controls allow customized result outputs for specific queries.

Does this UniProt REST API client require manual web browsing?▼

No, this Skill enables direct programmatic access to the UniProt REST API, bypassing manual web browsing for protein search, retrieval, and cross-database ID mapping. It provides a Python client for common operations using the requests dependency.

What are the limitations of using UniProt REST API for sequence retrieval?▼

Limitations depend on UniProt REST API rate limits and query complexity when performing batch retrieval or streaming large result sets. Users must manage scalability constraints and optional fields formatting within their Python client workflows.