Ucsc Genome MCP server

@pipeworx/ucsc-genome

Reference genome assemblies from the UCSC Genome Browser — which builds exist for a species, which annotation tracks sit on each build, the actual rows of any track over a genomic interval, and raw reference DNA.

Part of Pipeworx — an MCP gateway connecting AI agents to 1679+ live data sources.

Tools

danRer11), organism, scientific name, source assembly and release description. This is where you get the ID every other call keys on.

• ucsc_genomes(search?, limit?) — every UCSC assembly (~238), with its assembly ID (hg38, mm39,

name that ucsctrackdata wants. The browser UI shows labels, not names: "GENCODE V50" is track knownGene, and there is no rule that maps one to the other.

• ucsc_tracks(genome, search?, limit?) — annotation tracks on one assembly, with the INTERNAL track

interval: gene models with exon structure, ClinVar variants, repeats, whatever that track holds.

• ucsctrackdata(genome, track, chrom, start, end, maxItemsOutput?) — the track's rows over an

fraction and an N count.

• ucsc_sequence(genome, chrom, start, end, revComp?) — reference DNA for an interval, with GC

Auth

Keyless. No registration, no rate-limit headers observed. UCSC asks heavy users to mirror or use a local install rather than hammer the public endpoint, so keep interval widths sane.

Data sources

• — assembly catalogue.
• — track catalogue for one assembly.
• — track rows over an interval.
• — reference DNA.
• Docs:

Traps

genome is required on every coordinate tool and there is no default. hg19 (GRCh37) and hg38 (GRCh38) are different coordinate systems for the same genome, and every position is valid in both — so a wrong build never errors, it returns confident annotations for a different locus. BRCA1 sits at chr17:41,196,311-41,277,500 in hg19 and chr17:43,044,295-43,170,245 in hg38. Anything older than ~2018 (published tables, clinical spreadsheets, most dbSNP dumps) is hg19.

Coordinates are 0-based half-open; the Genome Browser UI is 1-based inclusive. A position copied out of the browser location box is one too high at the start.

Chromosomes need the chr prefix. UCSC wants chr17; Ensembl/NCBI style bare 17 is rejected.

Track search ranks by where the match landed, on purpose. hg38 carries ~24,000 tracks (most of them ENCODE subtracks) and the longLabels are prose, so a plain substring search for "gencode" matched 13,427 of them — and ~13,000 of those were false positives, because wgEncodeBroadHistone… lowercases to a string that literally contains "gencode". The ranking scores an internal-name hit above a shortLabel hit above prose, and treats a camelCase transition as a word boundary, which is what separates nmdEscGencode from wgEncode…. Without it the answer (knownGene) was on page 2,700.

Composite tracks nest their subtracks one level down inside the parent object. ucsc_tracks flattens them, otherwise a search for "clinvar" on hg38 misses every subtrack of the ClinVar container and reads as "UCSC does not have ClinVar".

getData/track keys its row array on the track name — usually. On some composites it keys on a subtrack instead, so the pack falls back to "the first array in the response" rather than reporting an empty result that is really a naming mismatch.

A bad assembly or track returns HTTP 400 with a useful error string in the JSON body — the pack surfaces that string, because "hg19 is not a valid track for genome hg38" is the whole diagnosis.

Quick Start

Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):

Shortened. The full README is on GitHub.