Can I perform local sequence alignments?

Yes, gget integrates high-performance tools like Muscle5 and DIAMOND for local protein and translated DNA alignment.

Does gget support protein structure prediction?

Yes, it includes built-in support for AlphaFold2, allowing you to predict and visualize 3D protein structures from amino acid sequences.

What databases can I access with gget?

gget provides a unified interface for over 20 major databases including Ensembl, UniProt, NCBI, ARCHS4, and the Protein Data Bank (PDB).

Is gget primarily for Python or the CLI?

All gget modules are designed to work interchangeably as both command-line tools and Python functions within scripts or Jupyter notebooks.

How often is the data in gget updated?

The tool is tested biweekly and updated to accommodate changes in the structure of the underlying biological databases it queries.

gget Bioinformatics Assistant

Name: gget Bioinformatics Assistant
Author: Yezez9

byYezez9

0•

Data Science & ML

Queries over 20 genomic databases for sequence analysis, protein structures, and gene metadata through a unified interface.

gget is a comprehensive bioinformatics tool designed to streamline the retrieval and analysis of genomic data. It provides researchers and developers with a consistent interface to access more than 20 major biological databases, including Ensembl, NCBI, and UniProt. By simplifying complex tasks—such as sequence alignment via BLAST, 3D protein structure prediction with AlphaFold, and gene expression analysis—into straightforward CLI commands and Python functions, gget accelerates the pace of computational biology workflows and ensures researchers are always working with the most current data.

Key Features

01High-speed sequence alignment using BLAST, BLAT, and DIAMOND

02Protein structure prediction and visualization with AlphaFold2

03Single-cell RNA-seq and tissue expression data querying

04Unified access to 20+ genomic and bioinformatic databases

050 GitHub stars

06Comprehensive gene/transcript metadata and FASTA sequence retrieval

Use Cases

01Retrieving reference genomes and gene annotations for pipeline development

02Conducting rapid sequence comparisons and multiple sequence alignments

03Predicting protein folding and identifying motifs for structural biology research

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add yezez9/research-agent gget

For use in Claude.ai and ChatGPT