gget

Query and analyze biological data from 20+ databases via Python or command line.

1|Updated Jan 14, 2026
One-click install
npx skills add https://github.com/Sologa/codex-pipeline --skill gget-sologa
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: gget
Source: https://github.com/Sologa/codex-pipeline/tree/main/.codex/skills/gget
Command: npx skills add https://github.com/Sologa/codex-pipeline --skill gget-sologa

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 genomic and proteomic data retrieval and analysis.

Core Features & Use Cases

  • Unified Access: Query Ensembl, UniProt, NCBI, PDB, AlphaFold, ARCHS4, and more through a single tool.
  • Diverse Analyses: Perform gene lookups, sequence retrieval, BLAST searches, structure prediction, expression analysis, and enrichment tests.
  • Use Case: Quickly find the protein sequence for a given gene, perform a BLAST search against the Swiss-Prot database, and retrieve its known 3D structure from the PDB, all within a few commands.

Quick Start

Use the gget skill to search for human genes related to 'GABA receptor' and display the top 5 results.

Frequently Asked Questions about gget

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

FAQPage Schema
How do I retrieve gene sequences and protein structures from multiple bioinformatics databases at once?

You can retrieve gene sequences and protein structures by using a unified command-line and Python interface that queries over 20 bioinformatics databases like Ensembl, UniProt, NCBI, and PDB simultaneously. This approach simplifies complex genomic and proteomic data retrieval into a few commands.

What is the best way to perform a BLAST search and functional enrichment analysis for a specific gene?

The best way to perform a BLAST search and functional enrichment analysis is to use an integrated bioinformatics tool that connects directly to databases like Swiss-Prot. This allows you to execute sequence searches and run enrichment tests seamlessly within a single workflow.

Can I query AlphaFold and ARCHS4 for protein structure prediction and gene expression analysis?

Yes, you can query AlphaFold and ARCHS4 for protein structure prediction and gene expression analysis. The tool provides a unified interface to access these specific genomic resources, facilitating both structural prediction and expression data retrieval.

Does this bioinformatics data retrieval tool require any external dependencies or API keys to function?

No external dependencies or API keys are required to function, as the tool operates with zero listed dependencies. You can immediately start querying biological data from over 20 bioinformatics databases without prerequisite environment setup.

How do I search for human genes related to a specific term like 'GABA receptor' and limit the results?

To search for human genes related to a specific term like 'GABA receptor' and limit the results, you can use the command-line interface to query gene information. This allows you to quickly find matching genes and display only the top results you need.