Can gget perform BLAST searches?

Yes, gget includes a dedicated module for BLASTing nucleotide and amino acid sequences against standard databases like nt, nr, and swissprot.

What data sources does gget access?

It accesses major bioinformatics databases including Ensembl, UniProt, NCBI, PDB, ARCHS4, and the CZ CELLxGENE Discover Census.

What is gget used for in Claude Code?

gget allows researchers to use Claude Code to query over 20 genomic databases, download reference genomes, and perform sequence alignments directly through the CLI.

How do I install gget for use with Claude?

You can install it using 'pip install gget' or 'uv pip install gget' in your local environment where Claude Code is active.

Does this skill support AlphaFold protein prediction?

Yes, gget provides a simplified interface for AlphaFold2 to predict 3D protein structures and generate PDB files.

gget Bioinformatics Toolkit

Name: gget Bioinformatics Toolkit
Author: lifangda

bylifangda

•

데이터 과학 및 ML

Provides unified access to 20+ genomic databases and bioinformatics tools for gene information, sequence analysis, and protein structure prediction.

소개

gget is a high-performance command-line and Python interface designed for bioinformaticians and researchers to efficiently query genomic data. It simplifies access to major databases like Ensembl, UniProt, and the PDB, while integrating advanced features like AlphaFold protein structure prediction, BLAST searches, and single-cell RNA-seq data retrieval. By automating complex workflows across multiple repositories, gget enables rapid sequence alignment, gene search, and metadata analysis directly from the terminal or within Python scripts, making it an essential tool for modern computational biology.

주요 기능

Gene expression analysis through ARCHS4 and CELLxGENE Discover Census
Reference genome metadata and FASTA sequence downloads
16 GitHub stars
High-speed BLAST and BLAT sequence alignment modules
Unified access to 20+ genomic and protein databases including Ensembl and UniProt
AlphaFold2 integration for automated 3D protein structure prediction

사용 사례

Predicting protein structures and eukaryotic linear motifs for novel amino acid sequences
Identifying gene orthologs and fetching sequences across multiple species for comparative genomics
Integrating large-scale genomic metadata into automated bioinformatics pipelines and notebooks

소개

주요 기능

Gene expression analysis through ARCHS4 and CELLxGENE Discover Census
Reference genome metadata and FASTA sequence downloads
16 GitHub stars
High-speed BLAST and BLAT sequence alignment modules
Unified access to 20+ genomic and protein databases including Ensembl and UniProt
AlphaFold2 integration for automated 3D protein structure prediction

사용 사례

Predicting protein structures and eukaryotic linear motifs for novel amino acid sequences
Identifying gene orthologs and fetching sequences across multiple species for comparative genomics
Integrating large-scale genomic metadata into automated bioinformatics pipelines and notebooks