What databases can gget access?

gget provides access to over 20 databases including Ensembl, UniProt, NCBI, PDB, AlphaFold, ARCHS4, Enrichr, OpenTargets, COSMIC, and CZ CELLxGENE.

Is gget suitable for both CLI and Python workflows?

Absolutely. Every gget module is designed to function both as a command-line tool and as a Python function, returning JSON/CSV or DataFrames respectively.

How does gget handle database structure changes?

gget modules are automatically tested on a biweekly basis and updated to ensure compatibility with the latest versions of the external databases they query.

Can I use gget for protein structure prediction?

Yes, gget includes a dedicated AlphaFold module for 3D protein structure prediction and a PDB module for querying the Protein Data Bank.

Bioinformatics & Genomics Toolkit (gget)

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

byMicrock

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Data Science & ML

Provides unified access to 20+ genomic databases for sequence analysis, protein structure prediction, and rapid bioinformatics queries.

About

gget is a specialized bioinformatics skill that integrates over 20 essential genomic databases and analysis tools into a single, consistent interface. It enables researchers and developers to perform complex tasks like BLAST searches, AlphaFold protein structure predictions, gene metadata retrieval, and single-cell RNA-seq data queries without switching between multiple web portals. Whether you are downloading reference genomes from Ensembl, aligning sequences with Muscle5, or exploring tissue-specific expression in ARCHS4, gget streamlines the computational biology workflow directly within your development environment.

Key Features

Protein structure prediction via AlphaFold2 and PDB metadata retrieval
81 GitHub stars
Reference genome downloads and comprehensive gene/transcript metadata extraction
Integration with large-scale expression data from ARCHS4 and CZ CELLxGENE Discover Census
Sequence analysis tools for BLAST, BLAT, and Multiple Sequence Alignment (Muscle/DIAMOND)
Unified access to 20+ genomic databases including Ensembl, UniProt, and NCBI

Use Cases

Querying single-cell expression data and gene correlations for transcriptomics and disease studies
Automating the retrieval of gene sequences and functional annotations for genomic research
Predicting 3D protein structures and identifying eukaryotic linear motifs for molecular analysis

About

Key Features

Protein structure prediction via AlphaFold2 and PDB metadata retrieval
81 GitHub stars
Reference genome downloads and comprehensive gene/transcript metadata extraction
Integration with large-scale expression data from ARCHS4 and CZ CELLxGENE Discover Census
Sequence analysis tools for BLAST, BLAT, and Multiple Sequence Alignment (Muscle/DIAMOND)
Unified access to 20+ genomic databases including Ensembl, UniProt, and NCBI

Use Cases

Querying single-cell expression data and gene correlations for transcriptomics and disease studies
Automating the retrieval of gene sequences and functional annotations for genomic research
Predicting 3D protein structures and identifying eukaryotic linear motifs for molecular analysis