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uniprot-protein-database

Query the UniProt REST API for protein sequences and annotations.

298|27|Updated Feb 18, 2026
Search Tags:#bioinformatics#protein database#sequence retrieval#proteomics#uniprot#id mapping
One-click install
npx skills add https://github.com/jaechang-hits/SciAgent-Skills --skill uniprot-protein-database
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: uniprot-protein-database
Source: https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/proteomics-protein-engineering/uniprot-protein-database
Command: npx skills add https://github.com/jaechang-hits/SciAgent-Skills --skill uniprot-protein-database

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill provides programmatic access to the UniProt protein database, enabling users to search for proteins, retrieve sequences, and map identifiers across different databases without manual web browsing.

Core Features & Use Cases

  • Protein Search: Find proteins using gene names, accession numbers, or functional keywords.
  • Sequence Retrieval: Download protein sequences in FASTA format.
  • ID Mapping: Convert identifiers between UniProt, Ensembl, PDB, and RefSeq.
  • Annotation Access: Retrieve functional annotations, GO terms, and protein features.
  • Use Case: Quickly find all human BRCA1 protein sequences and their corresponding PDB IDs for structural analysis.

Quick Start

Search for human insulin proteins using the UniProt REST API and print the first 500 characters of the results.

Frequently Asked Questions about uniprot-protein-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?▼

Retrieve protein sequences in FASTA format by querying the UniProt REST API with accession numbers or functional keywords, then downloading the returned sequence data programmatically.

Can I map protein identifiers between UniProt, Ensembl, and PDB?▼

Map protein identifiers between UniProt, Ensembl, PDB, and RefSeq by submitting accession numbers to the UniProt REST API, receiving cross-referenced database entries programmatically.

How do I search UniProt for proteins using gene names or functional keywords?▼

Search UniProt proteins by submitting gene names, accession numbers, or functional keywords to the REST API, receiving matching protein entries with detailed annotations, GO terms, and protein features.

Does this support batch processing for large proteomics datasets?▼

Batch process large proteomics datasets by utilizing the UniProt REST API's streaming and pagination options, selecting specific fields to manage and retrieve extensive protein data efficiently.

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

Limitations of using the UniProt REST API for sequence retrieval include network latency dependencies and pagination constraints, requiring streaming configurations and specific field selection to manage large proteomics datasets effectively.

Do I need pandas and requests to access UniProt protein annotations?▼

Access UniProt protein annotations by utilizing the requests library to query the REST API and pandas to structure the retrieved functional annotations, GO terms, and protein features for downstream analysis.

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