What is alterlab-gget?

A command-line and Python tool for looking up genes, DNA and protein sequences, protein structures, pathways, and related biology data across more than 20 databases. It gives these different sources a consistent way to query them.

Use it to find gene information from Ensembl, run BLAST searches, inspect AlphaFold protein structures, and check pathway or enrichment data from Enrichr.

It avoids learning separate tools and query formats for every biology database. It is suited to quick interactive lookups when you do not need a larger batch-processing workflow.

alterlab-gget — Skill for Claude Code by AlterLab-IEU

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent

npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-gget

Clone the repo

git clone --depth 1 https://github.com/AlterLab-IEU/AlterLab-Academic-Skills

Made for: Claude Code.

Or install alterlab-bioinformatics, the plugin that ships this one along with the rest of its 38 skills.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-gget/github.svg)](https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-gget)

Your own site

<a href="https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-gget"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-gget/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-gget"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-gget.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 94 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 1,425 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe. Third-party audits

NVIDIA SkillSpector pass 7 Sept 2026

How audits are shown

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.00094	$0.01425
Opus 5	$0.00047	$0.00713
Sonnet 5	$0.00019	$0.00285
Haiku 4.5	$0.00009	$0.00143

Measured 12d ago against content hash 982b60f4c7f9, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-11, from the pricing page.

Security

Grade A, and why

alterlab-gget scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 12d ago.

The scan reads SKILL.md. This mod also ships 3 executable files (scripts/batch_sequence_analysis.py, scripts/enrichment_pipeline.py, scripts/gene_analysis.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

skills/bioinformatics/alterlab-gget/SKILL.md · 124 lines

How it starts

The opening of the file, as written. The whole thing — 124 lines — stays where its author put it; the contents beside it link to each section on GitHub.

gget

Overview

gget is a command-line bioinformatics tool and Python package providing unified access to 20+ genomic databases and analysis methods. Query gene information, sequence analysis, protein structures, expression data, and disease associations through a consistent interface. All gget modules work both as command-line tools and as Python functions.

Important: The databases queried by gget are continuously updated, which sometimes changes their structure. gget modules are tested automatically on a biweekly basis and updated to match new database structures when necessary.

Installation

Install gget in a clean virtual environment to avoid conflicts:

# Install (or upgrade) into a clean environment
uv pip install --upgrade gget

# In Python/Jupyter
import gget

Quick Start

Basic usage pattern for all modules:

# Command-line
gget <module> [arguments] [options]

# Python
gget.module(arguments, options)

Most modules return:

Command-line: JSON (default) or CSV with -csv flag
Python: DataFrame or dictionary

Common flags across modules:

-o/--out: Save results to file
-q/--quiet: Suppress progress information
-csv: Return CSV format (command-line only)

Module Catalog

Pick a module, then see references/module_examples.md for worked CLI + Python examples and references/module_reference.md for the full parameter table.

Module	Purpose	Queried source
`ref`	Reference genome download links/metadata	Ensembl
`search`	Find genes by name/description	Ensembl
`info`	Gene/transcript metadata (~1000 IDs max)	Ensembl, UniProt, NCBI
`seq`	Nucleotide/amino-acid sequences (FASTA)	Ensembl
`blast`	BLAST against standard databases	NCBI BLAST
`blat`	Genomic position of a sequence	UCSC BLAT
`muscle`	Multiple sequence alignment	Muscle5 (local)
`diamond`	Fast local protein/translated alignment	DIAMOND (local)
`pdb`	Experimental protein structures + metadata	RCSB PDB
`alphafold`	Predict 3D protein structure (setup req.)	AlphaFold2 (local)
`elm`	Eukaryotic linear motifs (setup req.)	ELM
`archs4`	Correlated genes / tissue expression	ARCHS4
`cellxgene`	Single-cell RNA-seq (setup req.)	CZ CELLxGENE Census
`enrichr`	Ontology/pathway enrichment	Enrichr
`bgee`	Orthologs and expression	Bgee
`opentargets`	Disease/drug associations	OpenTargets
`cbio`	Cancer genomics heatmaps	cBioPortal
`cosmic`	Somatic cancer mutations (license/account)	COSMIC
`mutate`	Generate mutated sequences	local
`gpt`	Natural-language text generation (setup req.)	OpenAI API
`setup`	Install third-party deps for a module	local

Read the full file on GitHub · 124 lines

Files

What ships with it

8 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

12d ago First seen · 124 lines · 94 tokens per session scan A 982b60f4c7f9

Subscribe to this mod's changes

alterlab-gget is a skill published in the GitHub repository AlterLab-IEU/AlterLab-Academic-Skills (66 stars, last pushed 7d ago), licensed MIT. It adds 94 tokens to every session and 1,425 once invoked, about $0.0005 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

Research Scientific academic-research anthropic bioinformatics data-science prompt-engineering research-tools

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