Welcome!

gget is a free, open-source command-line tool and Python package that enables efficient querying of genomic databases.

gget consists of a collection of separate but interoperable modules, each designed to facilitate one type of database querying in a single line of code.

NOTE: The databases queried by gget are continuously being updated which sometimes changes their structure. gget modules are tested automatically on a biweekly basis and updated to match new database structures when necessary. If you encounter a problem, please upgrade to the latest gget version using pip install --upgrade gget. If the problem persists, please report the issue.

Request a new feature

gget info and gget seq are currently unable to fetch information for WormBase and FlyBase IDs (all other IDs are functioning normally). This issue arose due to a bug in Ensembl release 112. We appreciate Ensembl's efforts in addressing this issue and expect a fix soon. Thank you for your patience.

gget modules

These are the gget core modules. Click on any module to access detailed documentation.

gget alphafold Predict 3D protein structure from an amino acid sequence.	gget archs4 What is the expression of my gene in tissue X?	gget bgee Find all orthologs of a gene.	gget blast BLAST a nucleotide or amino acid sequence.
gget blat Find the genomic location of a nucleotide or amino acid sequence.	gget cbio Explore a gene's expression in the specified cancers.	gget cellxgene Get ready-to-use single-cell RNA seq count matrices from certain tissues/ diseases/ etc.	gget cosmic Search for genes, mutations, and other factors associated with certain cancers.
gget diamond Align amino acid sequences to a reference.	gget elm Find protein interaction domains and functions in an amino acid sequence.	gget enrichr Check if a list of genes is associated with a specific celltype/ pathway/ disease/ etc.	gget info Fetch all of the information associated with an Ensembl ID.
gget muscle Align multiple nucleotide or amino acid sequences to each other.	gget mutate Mutate nucleotide sequences based on specified mutations.	gget opentargets Explore which diseases and drugs a gene is associated with.	gget pdb Fetch data from the Protein Data Bank (PDB) based on a PDB ID.
gget ref Get reference genomes from Ensembl.	gget search Find Ensembl IDs associated with the specified search word.	gget seq Fetch the nucleotide or amino acid sequence of a gene.

If you use gget in a publication, please cite*:

Luebbert, L., & Pachter, L. (2023). Efficient querying of genomic reference databases with gget. Bioinformatics. https://doi.org/10.1093/bioinformatics/btac836

Read the article here: https://doi.org/10.1093/bioinformatics/btac836