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 infoandgget seqare 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