Is gget suitable for single-cell RNA-seq analysis?

Yes, it features a dedicated cellxgene module to query the CZ CELLxGENE Discover Census for single-cell data and metadata.

Can I use gget for protein structure prediction?

Yes, gget includes a simplified AlphaFold2 implementation for predicting 3D protein structures directly from amino acid sequences.

How does gget handle sequence alignment?

It supports standard BLAST, BLAT for genomic positions, Muscle5 for multiple sequence alignment, and DIAMOND for fast local protein alignment.

Does this skill work with Python?

Absolutely. gget is designed as both a CLI tool and a Python package, allowing for seamless integration into scripts and automated workflows.

What databases does gget support?

gget provides access to over 20 databases including Ensembl, UniProt, NCBI, AlphaFold, ARCHS4, Enrichr, OpenTargets, and the RCSB Protein Data Bank.

Bioinformatics & Genomics Toolkit (gget)

Name: Bioinformatics & Genomics Toolkit (gget)
Author: BbgnsurfTech

byBbgnsurfTech

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Data Science & ML

Provides rapid access to 20+ genomic databases and bioinformatics tools for gene searching, sequence alignment, and protein structure prediction.

About

gget is a high-performance CLI and Python toolkit that provides unified access to over 20 essential genomic databases, including Ensembl, UniProt, and NCBI. It enables researchers and developers to perform complex biological tasks such as gene searching, sequence alignment using BLAST/BLAT, protein structure prediction via AlphaFold, and single-cell RNA-seq data retrieval. By integrating these specialized capabilities into Claude, users can streamline scientific workflows, automate data fetching, and accelerate genomic analysis without manual database navigation or complex environment configuration.

Key Features

Automated reference genome downloads and sequence fetching for nucleotides and amino acids
Unified access to 20+ genomic databases like Ensembl, UniProt, and RCSB PDB
Protein structure prediction using simplified AlphaFold2 integration
Rapid BLAST/BLAT sequence alignment and multiple sequence alignment via Muscle5
3 GitHub stars
Comprehensive gene metadata retrieval including expression and tissue correlation data

Use Cases

Predicting protein structures and identifying eukaryotic linear motifs for structural biology
Automating the retrieval of gene sequences and metadata for large-scale genomic studies
Querying single-cell RNA-seq data and tissue-specific expression patterns for disease research

About

Key Features

Automated reference genome downloads and sequence fetching for nucleotides and amino acids
Unified access to 20+ genomic databases like Ensembl, UniProt, and RCSB PDB
Protein structure prediction using simplified AlphaFold2 integration
Rapid BLAST/BLAT sequence alignment and multiple sequence alignment via Muscle5
3 GitHub stars
Comprehensive gene metadata retrieval including expression and tissue correlation data

Use Cases

Predicting protein structures and identifying eukaryotic linear motifs for structural biology
Automating the retrieval of gene sequences and metadata for large-scale genomic studies
Querying single-cell RNA-seq data and tissue-specific expression patterns for disease research