UniProt — Protein Database

Overview

UniProt is the most comprehensive protein sequence and functional annotation database, containing 250M+ entries. This skill covers programmatic access via the UniProt REST API for protein search, sequence retrieval, ID mapping, and annotation queries. Swiss-Prot entries are manually curated; TrEMBL entries are computationally predicted.

When to Use

• Searching for proteins by gene name, accession, organism, or function keywords
• Retrieving protein sequences in FASTA format for downstream analysis
• Mapping identifiers between databases (UniProt ↔ Ensembl, PDB, RefSeq, KEGG)
• Accessing protein annotations: GO terms, domains, post-translational modifications
• Batch retrieving multiple protein entries for comparative analysis
• Downloading reviewed (Swiss-Prot) protein datasets for a specific organism
• For unified access to 40+ databases, use bioservices instead
• For protein 3D structures, use alphafold-database or pdb-database

Prerequisites