Can I use gget for both DNA and protein sequences?

Absolutely. gget includes tools like BLAST, BLAT, and Diamond that handle both nucleotide and amino acid sequences for various alignment and search tasks.

Can gget be used in Python scripts and the command line?

Yes, gget is designed as both a CLI toolkit and a Python package, with all modules functioning consistently across both environments.

What databases can I access with the gget skill?

gget provides access to over 20 scientific databases, including Ensembl, UniProt, AlphaFold, ARCHS4, Enrichr, OpenTargets, COSMIC, and the RCSB Protein Data Bank.

Does gget support protein structure prediction?

Yes, gget includes a specialized module for AlphaFold2 that allows you to predict 3D protein structures and generate visualizations directly from amino acid sequences.

How often are the gget database queries updated?

To maintain accuracy as external databases evolve, gget modules are automatically tested on a biweekly basis and updated to match new database structures.

Bioinformatics Data & Analysis (gget)

Name: Bioinformatics Data & Analysis (gget)
Author: Zehong-Wang

byZehong-Wang

0•

Data Science & ML

Provides a unified interface for rapid bioinformatics queries, genomic sequence analysis, and protein structure prediction across 20+ scientific databases.

gget is a versatile bioinformatics toolkit that streamlines research by providing programmatic and command-line access to over 20 specialized databases, including Ensembl, UniProt, and AlphaFold. It simplifies complex biological workflows such as retrieving reference genomes, performing BLAST searches, analyzing protein motifs, and querying single-cell RNA-seq data. This skill is essential for computational biologists and developers who need high-quality genomic and proteomic data integrated directly into their development environment or data pipelines without the friction of manual web-based searches.

Key Features

01Unified access to 20+ databases including Ensembl, UniProt, AlphaFold, and COSMIC

02Rapid sequence alignment and analysis via integrated BLAST, BLAT, and Muscle5

033D protein structure prediction and PDB metadata retrieval with AlphaFold2 support

04Comprehensive gene metadata extraction including synonyms, biotypes, and NCBI IDs

05Tissue-specific expression and single-cell RNA-seq data querying from ARCHS4 and CELLxGENE

060 GitHub stars

Use Cases

01Integrating real-time gene expression and disease association data into bioinformatics pipelines

02Automating the retrieval of reference genomes and gene annotations for multi-species analysis

03Performing rapid protein motif discovery and 3D structure prediction within a research workflow

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add zehong-wang/kosmos gget

For use in Claude.ai and ChatGPT

Download Skill