gget

Query over 20 bioinformatics databases for gene and protein data.

Updated Mar 10, 2026

Search Tags:#bioinformatics #protein structure #genomics #sequence analysis #database query #gene expression

Ready to run

npx skills add https://github.com/Yezez9/Research-Agent --skill gget-yezez9

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: gget
Source: https://github.com/Yezez9/Research-Agent/tree/main/scientific-skills/gget
Command: npx skills add https://github.com/Yezez9/Research-Agent --skill gget-yezez9

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill provides a unified command-line and Python interface to query over 20 bioinformatics databases, simplifying complex data retrieval and analysis for researchers.

Core Features & Use Cases

Fast Queries: Quickly access gene information, BLAST sequences, download protein structures, and perform enrichment analysis.
Multi-Database Access: Seamlessly query Ensembl, UniProt, NCBI, PDB, ARCHS4, CELLxGENE, and more from a single tool.
Use Case: A biologist needs to find the protein sequence for a specific gene, check its known disease associations, and find related research papers. This Skill can perform all these tasks with simple commands.

Quick Start

Use gget to find information about the human gene TP53.

Frequently Asked Questions about gget

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

FAQPage Schema

How do I query multiple bioinformatics databases for gene information and protein structures?▼

To query bioinformatics databases for gene information and protein structures, you can use a unified command-line and Python interface to retrieve data from over 20 sources like Ensembl, UniProt, and PDB. This tool simplifies complex data retrieval into simple commands.

What is the best way to retrieve gene expression data from ARCHS4 and CELLxGENE?▼

The best way to retrieve gene expression data from ARCHS4 and CELLxGENE is using a unified bioinformatics query tool that supports rapid expression data querying and enrichment analysis workflows from a single interface.

Can I perform sequence analysis and BLAST queries using Python?▼

Yes, you can perform sequence analysis and BLAST queries using Python. This Skill provides a Python interface to quickly access gene information, BLAST sequences, and download protein structures directly from databases like NCBI.

Does this bioinformatics database query tool support functional annotations and disease associations?▼

Yes, this bioinformatics database query tool supports functional annotations and disease associations. It facilitates rapid retrieval of gene information, sequence data, and known disease associations from databases like UniProt and Ensembl.

How do I download protein structures from PDB for biological research?▼

To download protein structures from PDB for biological research, use a unified command-line interface that facilitates rapid retrieval of structural data and functional annotations across over 20 bioinformatics databases.

Are there limitations when using a single interface to query NCBI and Ensembl databases?▼

When using a single interface to query NCBI, Ensembl, and other databases, limitations depend on the external database APIs and their rate limits. This tool relies on active connections to over 20 bioinformatics databases for real-time data retrieval.