"@context": https://schema.org
"@type": SoftwareApplication
"@id": https://github.com/longevity-genie/gget-mcp
identifier: longevity-genie/gget-mcp
name: Holy-BIO-MCP's gget server
description: >
A Model Context Protocol server for the gget bioinformatics library.
See details about gget: https://pachterlab.github.io/gget/
codeRepository: https://github.com/longevity-genie/gget-mcp
url: https://github.com/longevity-genie/gget-mcp/blob/main/README.md
maintainer:
- "@type": Person
name: Anton Kulaga
identifier: antonkulaga
url: https://github.com/antonkulaga
- "@type": Person
name: Newton Winter
identifier: winternewt
url: https://github.com/winternewt
license: https://spdx.org/licenses/MIT.html
applicationCategory: UtilitiesApplication
keywords:
- gget
- holy-bio-mcp
- bioinformatics
- genomics
- ncbi
- enrichr
- ensembl
- uniprot
- alphafold
- ucsc
datePublished: "2025-08-13"
operatingSystem:
- Cross-platform
programmingLanguage:
- Python
featureList:
- gget_search - General biological term search across gene names and descriptions using Ensembl database
- gget_search_genes - Enhanced gene symbol search with batch processing and descriptive term support
- gget_info - Detailed gene/transcript metadata retrieval using Ensembl IDs from multiple databases
- gget_seq - Fetch nucleotide/amino acid sequences (FASTA) from genes or transcripts via Ensembl
- gget_ref - Download reference genomes and annotations (GTF, FASTA) by species from Ensembl
- gget_blast - BLAST nucleotide/amino acid sequences against NCBI databases (nt, nr, swissprot)
- gget_blat - BLAT sequences against UCSC genome assemblies for genomic coordinate mapping
- gget_muscle - Multiple sequence alignment using MUSCLE v5 algorithm for DNA/protein sequences
- gget_diamond - Fast protein sequence alignment using DIAMOND algorithm with reference sequences
- gget_archs4 - Find correlated genes or tissue expression atlas using ARCHS4 RNA-seq database
- gget_enrichr - Functional enrichment analysis on gene lists using Enrichr (KEGG, GO, ChEA)
- gget_bgee - Get orthologs across species or expression data from Bgee comparative database
- gget_pdb - Query RCSB PDB for protein structures/metadata using PDB IDs
- gget_alphafold - Predict protein 3D structure using simplified AlphaFold v2.3.0 algorithm
- gget_elm - Predict Eukaryotic Linear Motifs from amino acid sequences or UniProt IDs
- gget_cosmic - Search COSMIC database for cancer mutations by gene symbol or download data
- gget_mutate - Apply mutations to nucleotide sequences using standard annotation formats
- gget_opentargets - Query OpenTargets for diseases, drugs, and clinical data by Ensembl ID
- gget_cellxgene - Query single-cell RNA-seq data from CZ CELLxGENE Discover using Census
- gget_setup - Install third-party dependencies for gget modules (alphafold, cellxgene, elm)
