What databases can gget access via Claude?

gget provides a unified interface to over 20 databases including Ensembl, UniProt, NCBI, RCSB PDB, ARCHS4, and CZ CELLxGENE.

Is there any specific setup required for advanced features?

Some advanced modules like AlphaFold and CELLxGENE require a one-time setup using the 'gget setup' command and specific dependencies like OpenMM.

Can I perform protein structure prediction with this skill?

Yes, gget includes a dedicated module for AlphaFold2 that allows for 3D protein structure prediction and result visualization.

In what format are the results returned?

Results are typically returned as JSON or CSV for command-line use, and as DataFrames or dictionaries when used within Python environments.

Is gget suitable for batch processing large genomic datasets?

gget is optimized for interactive exploration and quick lookups. For massive batch processing or highly complex workflows, it is often used alongside libraries like Biopython or Bioservices.

Bioinformatics Data Query (gget)

Name: Bioinformatics Data Query (gget)
Author: Sologa

bySologa

Data Science & ML

Accesses and analyzes data from over 20 genomic and proteomic databases through a unified interface.

About

gget is a specialized bioinformatics skill that integrates over 20 genomic and proteomic databases directly into the Claude environment. It enables researchers and developers to perform complex biological tasks—such as AlphaFold protein structure predictions, BLAST searches, and single-cell RNA-seq data retrieval—using a consistent, streamlined interface. By automating the fetching of gene metadata, sequences, and expression data, it eliminates the need for manual navigation through multiple disparate web portals, making it an essential tool for interactive scientific exploration and data analysis.

Key Features

0 GitHub stars
Unified access to 20+ genomic and proteomic databases including Ensembl, UniProt, and NCBI
Comprehensive gene searching and metadata extraction across multiple species
Integrated AlphaFold2 structure prediction and 3D protein visualization capabilities
Automated sequence analysis tools for BLAST, BLAT, and Muscle5 alignment
Access to large-scale expression data from ARCHS4 and CZ CELLxGENE Discover Census

Use Cases

Performing multiple sequence alignments and BLAST searches for evolutionary or comparative genomics
Retrieving detailed gene metadata and amino acid sequences for specific Ensembl IDs
Predicting 3D protein structures and identifying eukaryotic linear motifs (ELMs) for structural biology research

About

Key Features

0 GitHub stars
Unified access to 20+ genomic and proteomic databases including Ensembl, UniProt, and NCBI
Comprehensive gene searching and metadata extraction across multiple species
Integrated AlphaFold2 structure prediction and 3D protein visualization capabilities
Automated sequence analysis tools for BLAST, BLAT, and Muscle5 alignment
Access to large-scale expression data from ARCHS4 and CZ CELLxGENE Discover Census

Use Cases

Performing multiple sequence alignments and BLAST searches for evolutionary or comparative genomics
Retrieving detailed gene metadata and amino acid sequences for specific Ensembl IDs
Predicting 3D protein structures and identifying eukaryotic linear motifs (ELMs) for structural biology research