uniprot-database

Search UniProt proteins and retrieve FASTA sequences via REST API.

557|98|Updated Nov 7, 2025
One-click install
npx skills add https://github.com/jimmc414/Kosmos --skill uniprot-database-jimmc414
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: uniprot-database
Source: https://github.com/jimmc414/Kosmos/tree/main/kosmos-claude-scientific-skills/scientific-skills/uniprot-database
Command: npx skills add https://github.com/jimmc414/Kosmos --skill uniprot-database-jimmc414

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill provides direct access to the UniProt database, enabling users to search for proteins, retrieve sequences, map identifiers, and access detailed annotations programmatically.

Core Features & Use Cases

  • Protein Search: Find proteins by name, gene, accession, or functional annotations.
  • Sequence Retrieval: Obtain protein sequences in various formats (FASTA, etc.).
  • ID Mapping: Translate identifiers between UniProt and other biological databases.
  • Use Case: A researcher needs to find all human proteins associated with a specific Gene Ontology term and retrieve their sequences for further analysis.

Quick Start

Use the uniprot-database skill to search for human insulin proteins and retrieve their FASTA sequences.

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?

You can retrieve protein sequences in FASTA format from UniProt by using this Skill to query the UniProt REST API, fetching sequence data programmatically via Python scripting or direct HTTP requests.

Can I map protein identifiers between UniProt and other biological databases?

Yes, you can map protein identifiers between UniProt and other biological databases. This Skill performs cross-database ID mapping by submitting identifiers to the UniProt REST API endpoint.

What is the best way to search for human proteins associated with a specific Gene Ontology term?

The best way to search for human proteins by Gene Ontology term is to use this Skill to query the UniProt API, filtering entries by functional annotations to retrieve matching proteins and their sequences.

Does UniProt protein data retrieval require the requests library?

Yes, UniProt protein data retrieval requires the requests library. This Skill depends on the requests Python package to handle direct HTTP requests to the UniProt REST API for accessing entries and annotations.

How do I access detailed protein annotations programmatically for bioinformatics workflows?

You access detailed protein annotations programmatically by integrating this Skill into your Python bioinformatics workflows, sending targeted API requests to fetch UniProt entries rich in functional data.

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

Limitations of using the UniProt REST API for sequence retrieval include dependence on internet connectivity and the requests library, as this Skill does not cache data locally or support offline database access.