Description
gget is an agent skill for gget, a bioinformatics tool that works as both a command-line program and a Python package. It gives unified access to more than 20 genomic databases and analysis methods through one consistent interface. Its modules cover gene information, sequence analysis such as BLAST and BLAT, downloading viral sequences, protein structures in PDB and mmCIF formats, expression data, disease associations, and mouse tissue and cell specificity metrics. Most modules work as both command-line commands and Python functions. The skill warns that the databases gget queries change over time, which sometimes changes their structure. Its guidance targets gget 0.30.8, reviewed on 30 September 2026. For reproducible work, the skill advises pinning gget to that version, and for a broken upstream database adapter it says to update gget after checking the release notes. Installation is set out in a clean virtual environment, using Python 3.13 with uv, to avoid conflicts with other packages. Use it for quick lookups and retrievals from public biological databases. It is part of the k-dense-ai scientific agent skills repository on GitHub, which has about 49,600 stars.…
Highlights
- Access to 20+ genomic databases
- Command-line and Python use
- Gene info, BLAST and BLAT
- PDB and mmCIF structures
- Pinned to gget 0.30.8 for reproducibility
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gget FAQ
What is gget?
A bioinformatics tool that works as both a command-line program and a Python package, with access to more than 20 genomic databases and analysis methods.
What can I look up?
Gene information, sequence analysis such as BLAST and BLAT, viral sequences, PDB and mmCIF structures, expression data, disease associations and mouse tissue specificity.
Why does the skill recommend pinning a version?
The databases change over time, so the skill targets gget 0.30.8 and advises pinning it for reproducible work.
How should I install it?
In a clean virtual environment, using Python 3.13 with uv, to avoid conflicts.
How do I install the skill?
Run npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill gget.
Is it checked for security?
Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk.
What are the best gget alternatives?
Popular alternatives to gget include gget, biopython and bioservices. See all gget alternatives