What databases can gget access?

gget provides access to over 20 databases including Ensembl, UniProt, NCBI, RCSB PDB, ARCHS4, and CZ CELLxGENE Discover Census.

Does gget support sequence alignment?

Yes, gget supports multiple alignment tools including BLAST, BLAT, Muscle5 for multiple sequence alignment, and local alignment using DIAMOND.

Can I predict protein structures with this skill?

Yes, the gget alphafold module allows for 3D protein structure prediction, multimer modeling, and interactive visualization.

What data formats does gget return?

In CLI mode, gget returns JSON or CSV; in Python mode, it returns native dictionaries or Pandas DataFrames for easy analysis.

How often is the gget data updated?

The databases gget queries are continuously updated; gget modules are tested biweekly and updated to match new database structures automatically.

gget Bioinformatics Toolkit

Name: gget Bioinformatics Toolkit
Author: Activer007

byActiver007

データサイエンスとML

Provides rapid, unified access to over 20 genomic and proteomic databases for sequence analysis and protein structure prediction.

概要

gget is a comprehensive CLI and Python toolkit designed to streamline bioinformatics workflows by providing a consistent interface to major biological databases and computational tools. It enables researchers and developers to perform rapid BLAST searches, retrieve genomic metadata from Ensembl and UniProt, predict 3D protein structures using AlphaFold, and analyze single-cell RNA-seq data from CZ CELLxGENE. By automating database updates and providing results in standardized formats like JSON, CSV, or DataFrames, gget simplifies complex sequence analysis, structural biology, and gene expression queries without the overhead of manual data management or disparate API integrations.

主な機能

Rapid sequence alignment with BLAST, BLAT, Muscle5, and DIAMOND
Seamless 3D protein structure prediction via AlphaFold2 integration
Unified query access to 20+ databases including Ensembl, UniProt, and NCBI
Advanced gene expression and single-cell RNA-seq data retrieval
0 GitHub stars
Dual-mode interface supporting both CLI and Python environments

ユースケース

Querying tissue-specific gene expression correlations for medical research
Automating genomic metadata retrieval for large-scale bioinformatics pipelines
Performing rapid protein structure prediction and motif analysis within Python notebooks

概要

主な機能

Rapid sequence alignment with BLAST, BLAT, Muscle5, and DIAMOND
Seamless 3D protein structure prediction via AlphaFold2 integration
Unified query access to 20+ databases including Ensembl, UniProt, and NCBI
Advanced gene expression and single-cell RNA-seq data retrieval
0 GitHub stars
Dual-mode interface supporting both CLI and Python environments

ユースケース

Querying tissue-specific gene expression correlations for medical research
Automating genomic metadata retrieval for large-scale bioinformatics pipelines
Performing rapid protein structure prediction and motif analysis within Python notebooks