skills.rest
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alterlab-uniprot

Provides REST-based UniProt protein search, sequence retrieval, and ID mapping for Python workflows.

58|9|Updated Mar 16, 2026
Search Tags:#python#bioinformatics#rest-api#uniprot#id-mapping#sequence-retrieval#protein-search
One-click install
npx skills add https://github.com/AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-uniprot
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: alterlab-uniprot
Source: https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/tree/main/skills/databases/alterlab-uniprot
Command: npx skills add https://github.com/AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-uniprot

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Retrieves and orchestrates UniProt data programmatically via REST APIs, enabling researchers to search proteins, fetch sequences, and map identifiers without manual browsing.

Core Features & Use Cases

  • Protein search by name, gene, accession, or organism via the UniProt REST API.
  • Sequence retrieval in FASTA (and other supported formats) with optional field selection.
  • ID mapping between UniProt and external resources (PDB, Ensembl, RefSeq, etc.) for cross-database workflows.
  • Batch queries and streaming to support large datasets and integration into data pipelines.
  • Example workflow: search insulin, fetch its sequence, and map to a related resource.

Quick Start

Query a protein by accession and fetch its FASTA sequence.

Frequently Asked Questions about alterlab-uniprot

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

FAQPage Schema
How do I retrieve a protein sequence from UniProt using Python?▼

The Skill maps identifiers between UniProt and external databases like PDB, Ensembl, and RefSeq via the REST API. This facilitates cross-database workflows by translating accession numbers across different bioinformatics resources.

Can I batch query UniProt and stream results for large datasets?▼

Yes, this Skill supports UniProt batch queries and streaming endpoints. This allows you to handle large protein datasets efficiently and integrate retrieval directly into automated data pipelines.

Do I need the requests library to use this UniProt REST API client?▼

Yes, the Python requests library is required to run the provided client scripts. You must have this dependency installed to execute REST-based protein search, retrieval, and ID mapping tasks.

What is the best way to map protein IDs between UniProt and Ensembl?▼

The best way is using the UniProt REST API's ID mapping endpoint. This Skill provides a Python script to programmatically map identifiers between UniProt and external resources like Ensembl, PDB, and RefSeq.

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