skills.rest
silverstein
silversteinCOMMUNITY
Explore all skills by this author →
Website𝕏@matsilversteinGitHub

uniprot-database

Automate UniProt protein search, sequence retrieval, and ID mapping via REST endpoints.

21|2|Updated Dec 8, 2025
Search Tags:#bioinformatics#rest api#uniprot#protein search#id mapping#python requests#fasta retrieval
One-click install
npx skills add https://github.com/silverstein/claude-scientific-skills-desktop --skill uniprot-database-silverstein
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: uniprot-database
Source: https://github.com/silverstein/claude-scientific-skills-desktop/tree/main/corpus/uniprot-database
Command: npx skills add https://github.com/silverstein/claude-scientific-skills-desktop --skill uniprot-database-silverstein

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

UniProt-specific API access is hard to use consistently when you need reliable protein searches, FASTA retrieval, and cross-database identifier mapping.

Core Features & Use Cases

  • Protein search & retrieval: Find proteins by accession, gene name, or organism and retrieve entries in formats like FASTA.
  • Batch workflows & ID mapping: Map UniProt accessions to other databases (e.g., PDB) using the UniProt ID mapping service.
  • Scalable downloads: Stream large result sets for proteome-scale extraction without manual pagination.

Real-world use case: you have a list of UniProt accessions from an experiment, map them to PDB identifiers, then fetch the corresponding sequences and annotations for downstream analysis.

Quick Start

Ask the AI to search UniProt for reviewed human proteins matching a query and return the results in TSV with only the fields you specify.

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 using the UniProt REST API?▼

To retrieve FASTA sequences from the UniProt REST API, you query the uniprotkb fetch endpoint with specific protein accessions. This automates sequence retrieval for bioinformatics workflows without manual downloads.

How do I map UniProt accessions to PDB identifiers in batch?▼

Batch ID mapping translates UniProt accessions to cross-database identifiers like PDB by submitting jobs to the UniProt idmapping service. You run the job, check its status, then retrieve the mapped results output.

What is the best way to download large protein datasets from UniProt without manual pagination?▼

Streaming large result sets from UniProt allows proteome-scale extraction without manual pagination. By applying stream queries to the REST API, you efficiently download complete search results.

Can I search UniProt for reviewed human proteins and return specific fields in TSV?▼

UniProt REST API search supports field selection with explicit output formats like TSV. You can query for reviewed human proteins and return only the specific annotation fields you specify.

Does the UniProt ID mapping service support cross-database identifier mapping for bioinformatics workflows?▼

The UniProt ID mapping service supports cross-database identifier mapping for bioinformatics workflows. It maps accessions from experiments to external databases, fetching corresponding sequences and annotations for downstream analysis.

Why does my UniProt search return too many results to process at once?▼

Large UniProt search queries can overwhelm standard pagination limits. Applying optional stream queries to the REST API handles large result sets efficiently, enabling scalable downloads for proteome-scale extraction.

Related Skills

Explore More Education & Research Skills→
Runchuan-BURunchuan-BU
401

query-uniprot

Retrieve protein sequences and functional annotations from the UniProt REST API.

Community
Intermediate
jaechang-hitsjaechang-hits
298

prokka-genome-annotation

Annotate prokaryotic genomes with Prokka, identifying genes and outputting GFF3, GenBank, FASTA, and TSV files.

Community
Intermediate
yf8578yf8578
1

biopython

Parse FASTA, GenBank, and PDB files for molecular biology analyses.

Community
Advanced
jimmc414jimmc414
557

uniprot-database

Search UniProt proteins and retrieve FASTA sequences via REST API.

Community
Intermediate