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UCSC Table Browser API — programmatic access to the UCSC Genome Browser's track data via REST endpoints. Retrieve genomic sequences, annotation tracks, gene models, conservation scores, and regulatory
Use with AI
Install the MCP server or CLI to instantly fetch UCSC Table Browser API documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/table-browser-api
Ensembl Database — EMBL-EBI's comprehensive genome annotation database covering 300+ species with gene models, variants, regulatory features, and comparative genomics. Query via REST API at rest.ensem
1 shared topic • 2 shared operations
gffread -- GFF/GTF utility for filtering, converting, and extracting sequences from genome annotation files. Converts between GFF3 and GTF formats, extracts transcript (FASTA) and protein sequences fr
1 shared topic • 2 shared operations
Liftoff — accurate genome annotation liftover tool that maps GFF/GTF annotations between assemblies of the same or closely-related species using Minimap2 alignment. Supports gene copy detection, ORF v
1 shared topic • 2 shared operations
MAKER — portable genome annotation pipeline that integrates ab initio gene predictors (SNAP, Augustus, GeneMark), protein and EST evidence alignment, and repeat masking to produce GFF3 gene models wit
1 shared topic • 2 shared operations
ncbi-genome-download is a Python CLI tool and library for bulk downloading genome sequences and associated files from NCBI RefSeq and GenBank FTP servers. Supports all taxonomic groups (bacteria, fung
1 shared topic • 2 shared operations