skills.rest
silverstein
silversteinCOMMUNITY
Explore all skills by this author →
Website𝕏@matsilversteinGitHub

gget

Retrieve genomic, sequence, structural, and functional evidence for genes and proteins via unified gget modules.

21|2|Updated Dec 8, 2025
Search Tags:#bioinformatics#protein structure#sequence retrieval#BLAST#expression analysis#gene search#disease associations
One-click install
npx skills add https://github.com/silverstein/claude-scientific-skills-desktop --skill gget-silverstein
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: gget
Source: https://github.com/silverstein/claude-scientific-skills-desktop/tree/main/corpus/gget
Command: npx skills add https://github.com/silverstein/claude-scientific-skills-desktop --skill gget-silverstein

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

gget eliminates the time-consuming chore of stitching together multiple bioinformatics tools and APIs by providing a single, consistent interface for common genomic, sequence, and analysis queries.

Core Features & Use Cases

  • Unified gene and database querying: Search genes, retrieve gene/transcript metadata, and get sequences with consistent module interfaces.
  • Sequence analysis and similarity: Run BLAST/BLAT and perform multiple sequence alignment workflows without manual format wrangling.
  • Structure, motifs, and expression context: Pull structure metadata, run simplified AlphaFold workflows, predict eukaryotic linear motifs, and query expression/correlation and disease/drug associations.
  • Use Case: You have a gene name list and need results that include Ensembl identifiers, protein sequences, BLAST hits, and disease associations; use gget modules to generate the full, connected evidence set.

Quick Start

Use gget to search for genes by name in human for the terms BRCA and cancer by running: gget search -s homo_sapiens BRCA cancer.

Frequently Asked Questions about gget

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I retrieve protein sequences and gene metadata for a list of gene names?▼

You can retrieve protein sequences and gene metadata by querying gene names through a unified bioinformatics interface, returning Ensembl identifiers, transcript metadata, and associated sequences in a single connected result set.

Can I run BLAST similarity searches and fetch disease associations together?▼

BLAST similarity searches and disease association lookups can be executed together through a single toolkit, eliminating the need to manually stitch together multiple APIs and separate analysis tools.

What's the best way to query gene expression correlation and predict eukaryotic motifs?▼

Querying expression correlation and predicting eukaryotic linear motifs are supported through dedicated modules, allowing you to mine expression data and predict motifs without manual format conversion.

Do I need to set up AlphaFold separately to pull protein structure metadata?▼

AlphaFold structure workflows require an optional one-time setup, along with similar setup for modules like elm or cellxgene, before pulling simplified structure metadata and running structural queries.

How does a unified genomics interface compare to running separate bioinformatics tools?▼

A unified genomics interface provides a consistent module interface for gene discovery, sequence retrieval, and BLAST searches, replacing the time-consuming chore of manually wrangling formats across multiple independent tools.

Why does my gene search require specific identifiers and parameters per module?▼

Gene search requires correct identifiers and parameters per module to accurately query underlying genomic databases, ensuring that sequence retrieval, BLAST, and expression mining return valid evidence.

Related Skills

Explore More Education & Research Skills→
ovachieverovachiever
52

gget

Query genomic data across multiple databases via CLI and Python interfaces.

Community
Advanced
jimmc414jimmc414
557

gget

Query over 20 genomic databases via command-line and Python interfaces.

Community
Advanced
jasrajtulsijasrajtulsi

gget

Query and synthesize bioinformatics database results for genes, proteins, and sequences.

Community
Advanced
jaechang-hitsjaechang-hits
298

gget-genomic-databases

Query over 20 genomic and biological databases via command-line or Python interface.

Community
Intermediate