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gget

Query 20+ bioinformatics databases for genes, sequences, structures, and expression data.

Updated Apr 18, 2026
Search Tags:#bioinformatics#genomics#alphafold#blast#gene expression#enrichment analysis#sequence alignment
One-click install
npx skills add https://github.com/ppavlidis/skillz --skill gget-ppavlidis
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: gget
Source: https://github.com/ppavlidis/skillz/tree/main/skills/gget
Command: npx skills add https://github.com/ppavlidis/skillz --skill gget-ppavlidis

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires gget, pandas, and includes scripts (resource) and references (resource) components.

What problem does it solve? Bioinformatics research requires querying dozens of disparate databases (Ensembl, UniProt, NCBI, AlphaFold, Enrichr, ARCHS4, and more), each with its own API and data format. This Skill provides a unified command-line and Python interface to all of them, eliminating the need to learn and integrate each database separately. ## Core Features & Use Cases - Gene & Reference Queries: Search genes by name, fetch Ensembl reference genomes, retrieve gene/transcript metadata, and download nucleotide or protein sequences in FASTA format. - Sequence & Structure Analysis: Run BLAST/BLAT searches, multiple sequence alignment with Muscle5, fast local alignment with DIAMOND, AlphaFold2 structure prediction, and ELM motif detection. - Expression, Enrichment & Disease Data: Query ARCHS4 tissue expression, CELLxGENE single-cell data, Enrichr pathway enrichment, OpenTargets disease/drug associations, cBioPortal cancer genomics, and COSMIC mutations. - Use Case: Given a gene symbol like ACE2, retrieve its Ensembl ID, protein sequence, tissue expression profile, top correlated genes, disease associations, and known drug targets in a single scripted workflow. ## Quick Start Ask the AI to use gget to search for the gene ACE2 in human and retrieve its protein sequence and tissue expression data.

Frequently Asked Questions about gget

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

FAQPage Schema
How do I search for a gene and get its sequence with gget?▼

Use gget search with the gene name and species to get the Ensembl ID, then pass that ID to gget seq to retrieve the nucleotide sequence. Add the translate flag to get the amino acid sequence instead.

What databases can gget query for bioinformatics analysis?▼

gget queries over 20 databases including Ensembl, UniProt, NCBI, RCSB PDB, ARCHS4, CELLxGENE, Enrichr, Bgee, OpenTargets, cBioPortal, and COSMIC. It also runs BLAST, BLAT, Muscle5, DIAMOND, and AlphaFold2 analyses.

gget vs biopython for batch sequence processing?▼

gget is best for interactive exploration and quick lookups across many databases with a simple interface. For batch processing or advanced BLAST workflows, biopython is recommended; for multi-database Python pipelines, consider bioservices.

Does gget alphafold work without extra setup?▼

No, AlphaFold prediction requires installing OpenMM first and then running gget setup alphafold, which downloads roughly 4GB of model parameters. The cellxgene, elm, and gpt modules also require a one-time setup step.

Why does gget cellxgene fail to find my gene?▼

Gene symbols in gget cellxgene are case-sensitive: use PAX7 for human and Pax7 for mouse. Alternatively, pass Ensembl IDs with the ensembl flag to avoid symbol casing issues entirely.

Can I use gget COSMIC queries for commercial projects?▼

COSMIC requires a registered account and license fees apply for commercial use, though it is free for academic use. You must download the COSMIC database with your credentials before running any queries.

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