Can I use gget for protein structure prediction?

Yes, gget includes a simplified AlphaFold2 module for predicting 3D protein structures and can generate PDB files and 3D visualizations.

What databases can the gget skill access?

gget provides a unified interface to over 20 databases including Ensembl, UniProt, AlphaFold, NCBI, PDB, ARCHS4, and CZ CELLxGENE.

Is gget suitable for high-throughput batch processing?

While gget is optimized for rapid queries and ease of use, the documentation recommends using Biopython or bioservices for extremely advanced or large-scale batch processing.

Does gget support both CLI and Python usage?

Absolutely. All gget modules are designed to work interchangeably as command-line tools and as Python functions, returning JSON/CSV or DataFrames respectively.

Bioinformatics Toolkit (gget)

Name: Bioinformatics Toolkit (gget)
Author: Microck

byMicrock

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Data Science & ML

Retrieves genomic, transcriptomic, and proteomic data from 20+ bioinformatics databases using a unified interface.

gget empowers Claude with specialized bioinformatics capabilities, enabling rapid querying of biological databases directly from command-line or Python environments. It provides seamless access to Ensembl gene information, AlphaFold protein structures, NCBI sequences, and single-cell RNA-seq data from CELLxGENE. Whether performing BLAST searches, multiple sequence alignments, or downloading reference genomes, gget streamlines complex biological data retrieval tasks into simple, consistent commands, making it an essential tool for computational biologists and life science researchers.

Key Features

013D protein structure prediction and visualization via AlphaFold2 integration

02Rapid BLAST and BLAT searches for nucleotide and amino acid sequences

03Automated reference genome metadata and sequence file downloads

04Querying of single-cell RNA-seq data and tissue-specific expression atlases

05Unified access to 20+ biological databases including Ensembl, UniProt, and PDB

0681 GitHub stars

Use Cases

01Predicting protein structures and eukaryotic linear motifs for molecular modeling

02Automating gene sequence retrieval and sequence alignment for genomic research

03Analyzing gene correlation and tissue-specific expression in disease studies

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add microck/ordinary-claude-skills gget

For use in Claude.ai and ChatGPT

Download Skill