uniprot-database

Topics in the source

• UniProt Database
• Overview
• When to Use This Skill
• Core Capabilities
• 1. Searching for Proteins
• 2. Retrieving Individual Protein Entries
• 3. Batch Retrieval and ID Mapping
• 4. Streaming Large Result Sets

UniProt is the world's leading comprehensive protein sequence and functional information resource. Search proteins by name, gene, or accession, retrieve sequences in FASTA format, perform ID mapping across databases, access Swiss-Prot/TrEMBL annotations via REST API for protein analysis. This skill should be used when: Searching for protein entries by name, gene symbol, accession, or organism Retrieving protein sequences in FASTA or other formats Mapping identifiers between UniProt and external databases (Ensembl, RefSeq, PDB, etc.) Accessing protein annotations including GO terms, domains, and functional descriptions Batch retrieving multiple protein entries efficiently Querying reviewed (Swiss-Prot) vs. unreviewed (TrEMBL) protein data Streaming large protein datasets Building custom queries with field-specific search syntax Search UniProt using natural language queries or structured search syntax. Common search patterns: Use the API search endpoint: https://rest.uniprot.org/uniprotkb/search?query={query}&format={format} Supported formats: JSON, TSV, Excel, XML, FASTA, RDF, TXT Retrieve specific protein entries by accession number. Accession number formats: Classic: P12345, Q1AAA

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