gget
Category: scientific-databases · License: BSD-2-Clause license · Version: 1.5 · Includes scripts
Tags: bioinformatics databases, Ensembl, BLAST, AlphaFold, gene lookup
When to use it
Queries 20+ bioinformatics databases and analysis services through the gget CLI and Python package, covering Ensembl gene search, info and sequences (ref, search, info, seq), BLAST, BLAT, MUSCLE, DIAMOND, PDB, AlphaFold, ELM, ARCHS4, CELLxGENE, Enrichr, Bgee, OpenTargets, cBioPortal, COSMIC, viral sequence downloads (virus), and 8cube mouse specificity and expression data. Use when looking up gene or transcript details, running a quick BLAST/BLAT search, fetching AlphaFold or PDB structures, running enrichment analysis on a gene list, downloading viral sequences with filters, or exploring disease and drug associations interactively. Not for batch processing or fine-grained BLAST control (use biopython) or multi-database Python pipelines (use bioservices).Example requests
Ask your agent in plain language, for example:- “quick blast of this protein sequence against nr: MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQ”
- “I have a list of 150 differentially expressed genes from my mouse liver RNA-seq in de_genes.txt (gene symbols). I’m on a cluster node with pip. Can you run GO biological process and KEGG enrichment on them directly from the terminal and save a CSV? I’d also like to see the top 10 terms.”
- “I’m studying a possible drug target, EGFR. What diseases and drugs are linked to it, and is there a predicted or experimental 3D structure I could look at?”
Install
/plugin marketplace add KalarisLabs/research-agent-skills and install the whole scientific-databases category with /plugin install scientific-databases@research-agent-skills.