uniprot-database

Query UniProt REST endpoints to search entries, retrieve FASTA sequences, and map identifiers.

1|Updated Mar 4, 2026

Search Tags:#bioinformatics #rest-api #batch-processing #protein #uniprot #id-mapping #fasta

Ready to run

npx skills add https://github.com/Hung-3008/agusta --skill uniprot-database-hung-3008

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: uniprot-database
Source: https://github.com/Hung-3008/agusta/tree/main/.agents/skills/uniprot-database
Command: npx skills add https://github.com/Hung-3008/agusta --skill uniprot-database-hung-3008

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Direct UniProt REST API access to protein data including searching entries, retrieving sequences in FASTA format, and performing ID mappings across databases.

Core Features & Use Cases

Protein search by name, accession, organism, and GO terms.
Retrieve protein sequences in FASTA or other formats.
Batch retrieval and ID mapping between UniProt and external resources (Ensembl, RefSeq, PDB, GO, etc.).
Access Swiss-Prot (reviewed) vs. TrEMBL (unreviewed) annotations.
Streaming large result sets for big datasets.

Quick Start

Query UniProt REST endpoints to search entries, retrieve sequences, and map identifiers for automated workflows.

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?▼

To retrieve FASTA protein sequences, query the UniProt REST API endpoints directly using HTTP requests. The Skill provides Python helper scripts to automate this process, supporting both single entry retrieval by accession and batch processing for large datasets.

Can I map UniProt IDs to Ensembl, RefSeq, and PDB databases?▼

You can map UniProt identifiers to Ensembl, RefSeq, PDB, and GO terms using the UniProt REST API ID mapping functionality. The Skill includes helper functions and references to supported mapping databases to enable cross-database identifier translation.

How do I batch search UniProt entries by organism and GO terms?▼

UniProt batch search by organism and GO terms is performed by constructing specific query syntax against the UniProt REST API. The Skill supports field customization and streaming of large result sets to handle extensive protein datasets efficiently.

Does the UniProt REST API support streaming for large result sets?▼

The UniProt REST API supports streaming large result sets for batch retrieval workflows. This Skill enables streaming to handle big datasets when searching protein entries or retrieving sequences, preventing memory bottlenecks during automated processing.

What's the difference between Swiss-Prot reviewed and TrEMBL unreviewed annotations in UniProt?▼

Swiss-Prot contains reviewed protein annotations curated by experts, while TrEMBL holds unreviewed computationally generated entries. The Skill provides direct REST access to both datasets, allowing you to filter queries and retrieve entries based on annotation quality.

Do I need the requests library to query the UniProt REST API in Python?▼

You need the Python requests library to use this Skill, as it handles direct HTTP/REST queries against UniProt endpoints. The Skill includes Python client scripts with helper functions built on requests to search entries, map IDs, and retrieve sequences.