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uniprot

Fetch protein sequences, annotations, and PDB cross-references from UniProt via REST API.

25|5|Updated Mar 22, 2026
Search Tags:#bioinformatics#sequence#annotation#pdb#uniprot#domain-boundaries
One-click install
npx skills add https://github.com/zongtingwei/Bioclaw_Skills_Hub --skill uniprot-zongtingwei
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: uniprot
Source: https://github.com/zongtingwei/Bioclaw_Skills_Hub/tree/main/skills/protein-design/skills/uniprot
Command: npx skills add https://github.com/zongtingwei/Bioclaw_Skills_Hub --skill uniprot-zongtingwei

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Provide a streamlined method to fetch protein sequences, annotations, and cross-references from UniProt for downstream design, analysis, and integration into pipelines.

Core Features & Use Cases

  • Retrieve sequences by accession or gene name.
  • Access domain boundaries and functional annotations.
  • Cross-reference to PDB structures for structure-guided design.

Quick Start

Query UniProt for the sequence and domain annotations of a given accession and return both FASTA and JSON formats for immediate downstream use.

Frequently Asked Questions about uniprot

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

FAQPage Schema
How do I retrieve protein sequences and annotations from UniProt programmatically?▼

To retrieve UniProt sequences and annotations programmatically, query the REST API by accession or gene name to fetch data in JSON and FASTA formats, validating responses to ensure usable results for downstream design workflows.

Can I get domain boundaries and functional annotations for a specific protein accession?▼

Yes, you can retrieve domain boundaries and functional annotations by querying the UniProt REST API with a specific accession, returning structured JSON data that details the protein's sequence features and cross-references.

How do I cross-reference UniProt entries to PDB structures for structure-guided design?▼

Cross-reference UniProt entries to PDB structures by querying the UniProt REST API, which returns mapped PDB identifiers within the JSON response to support structure-guided design workflows across diverse organisms.

Does this UniProt retrieval method return data in both FASTA and JSON formats?▼

Yes, the UniProt retrieval method returns data in both FASTA and JSON formats, handling responses from the REST API to provide sequences and structured annotations for immediate downstream use and pipeline integration.

Do I need REST API access to fetch UniProt sequences and cross-references?▼

Yes, you need REST API access to fetch UniProt sequences, annotations, and cross-references, as the retrieval process queries the API endpoints and validates the returned JSON and FASTA responses.

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