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gget Bioinformatics Queries

Query 20+ bioinformatics databases (genes, BLAST, PDB, enrichment) from the agent

Source Download skill
Repository
K-Dense-AI/scientific-agent-skills
Stars
55,780
Licence
MIT
Files
9 files

What it does

Teaches the agent to use gget, a command-line tool and Python package that gives one consistent interface to many public genomics databases. Once installed, the agent can look up gene information, run BLAST or BLAT searches, download viral sequences, fetch protein structures, run enrichment analysis and query resources such as Open Targets, COSMIC and CELLxGENE, instead of guessing at database formats. It also carries reference notes and example scripts for batch sequence analysis, gene analysis and enrichment pipelines.

Great for

  • Bioinformatics students or researchers doing interactive gene and protein exploration
  • Developers building simple scripted lookups against public genomics databases
  • Analysts who need a quick enrichment analysis of a gene list with reproducible settings

Skip it if

  • Large batch or high-throughput pipelines, where the skill itself recommends biopython instead (gget is aimed at interactive and simple queries)
  • Clinical or diagnostic decisions: results come from live public databases that change over time and are not validated for medical use
  • Anyone without network access, since most functions query remote servers

Try asking

  • “Look up the function and transcript information for the human gene TP53 and save it as CSV”
  • “Run an Enrichr enrichment analysis on this list of 50 gene symbols against a named human library”
  • “Find PDB structures for a given protein and download the mmCIF file”
  • “Run a BLAST search for this protein sequence and summarise the top hits”
Step-by-step guide: how to use gget Bioinformatics QueriesInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 9 original files, the MIT licence and an attribution note.

    gget.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip gget.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip gget.zip -d .claude/skills/

    Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.

  3. 3

    Ask for the task

    No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.

Get better results

  • Pin gget==0.30.8 in a clean virtual environment so results stay reproducible, and record database versions and dates with your output
  • Ask the agent to select exact gene_name matches and to report mapped and unmapped counts, rather than trusting the first search hit
  • Avoid the deprecated alphafold and gpt modules; the skill says they are legacy and no longer maintained upstream

What's inside

  • references/common_workflows.md
  • references/database_info.md
  • references/module_catalog.md
  • references/module_reference.md
  • references/workflows.md
  • scripts/batch_sequence_analysis.py
  • scripts/enrichment_pipeline.py
  • scripts/gene_analysis.py
  • SKILL.md

Redistributed unmodified from K-Dense-AI/scientific-agent-skills under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.