Ucsc Genome
NPM · @PIPEWORX/MCP-UCSC-GENOME · 2 COMPONENTS
UCSC Genome Browser REST API — reference genome assemblies for ~250 species, the annotation tracks…
Available components
Last scanned (14 hours ago)
Scores higher than 72% of npm servers
Category Health and Science
How this component scores in each security and reliability category. Every signal is checked automatically from public evidence about the published package, including repeated runs of it in an isolated sandbox, and we only credit what we can confirm. How we score → Why this is hard to score →
Supply Chain Security100
- No malware found by supply-chain analysis.Pass
- No known CVEs affecting this package version or its production dependencies.Pass
- No install/post-install scripts declared.Pass
- No production dependencies, so there is no dependency health to assess. View diagnostics → Pass
Provenance & Transparency97
- Source repository is publicly reachable at the declared URL. View diagnostics → Pass
- Cryptographically verified build provenance (signed, bound to pipeworx-io/mcp-ucsc-genome). View diagnostics → Pass
- Clear OSI-approved license (MIT).Pass
- Actively maintained (last published 6 days ago).Pass
- Disclosure check failed: no security disclosure policy was found in the source repository. See how to fix → Fail
Schema Quality & AI Usability61
- AI-judged instruction clarity (excellent).Pass
- Context-footprint check failed: tool/resource definitions use about 1446 tokens (~361/item across 4 items; 4 tools + 0 resources), over budget; trim descriptions and params. See how to fix → Fail
- Usage-examples check failed: none of the tools include examples. See how to fix → Fail
Stability & Change Management23
- Stability observed for 7 of 30 days with no destabilising changes; credit accrues until the full window elapses.Partial
Tool Coverage100
- 100% of tools have a non-trivial description (not blank, and not just the tool's name).Pass
- 100% of tool parameters carry a description.Pass
Tool Safety100
- No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.Pass
- We read all 4 captured tool definition(s), and no name or description among them implies an irreversible operation.Pass
- An AI judge read all 5 captured unit(s) of tool text and found none that tries to manipulate the model reading it.Pass
Capabilities100
- Implements a supported MCP spec version (2025-11-25); the latest is 2026-07-28.Pass
Checks we ran (16)
- Malware scan
- Known CVEs
- Install scripts
- Dependency health
- Source repository
- Provenance
- License
- Maintenance
- Security disclosure
- Schema quality
- Stability
- Tool coverage
- Injection markers
- Destructive annotations
- Judged manipulation
- MCP protocol
Does not apply to this package (2)
- Endpoint SecurityScored on hosted endpoints only. A package has no live endpoint of its own for us to probe.
- Transport & ReachabilityScored on hosted endpoints only. A package has no live endpoint of its own for us to probe.
The score does not measure everything. What the score does not measure →
Every change we have recorded for this component, newest first. Security-relevant changes are always shown. ▲ marks a change for the better, ▼ a change for the worse; unmarked changes are neutral.
- 5 Nov 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 20 to 23. That category is still filling its 30-day observation window: 6 days of observed history at the previous scan, 7 at this one. The score rises as the window fills, whether or not the server changes.
- 3 Nov 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 13 to 17. That category is still filling its 30-day observation window: 4 days of observed history at the previous scan, 5 at this one. The score rises as the window fills, whether or not the server changes.
- 1 Nov 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 7 to 10. That category is still filling its 30-day observation window: 2 days of observed history at the previous scan, 3 at this one. The score rises as the window fills, whether or not the server changes.
- 30 Oct 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 0 to 3. That category is still filling its 30-day observation window: 0 days of observed history at the previous scan, 1 at this one. The score rises as the window fills, whether or not the server changes.
- 29 Oct 26 78
First indexed and scored.
Diagnostic detail from the automated scan of this channel: what the scanner observed at each step, so you can see exactly where a check passed or failed. It is informational only and never changes the trust score.
Captured 5 Nov 2026 · Analysed npm/@pipeworx/mcp-ucsc-genome@0.2.0
Provenance Verified
A signed build attestation was found and verified, binding this exact artifact to the source repository it claims to come from.
| Result | Verified |
|---|---|
| Ecosystem | npm |
| Reason | Verified |
| Discovered via | Registry attestation endpoint |
| Source repo | pipeworx-io/mcp-ucsc-genome |
| Certificate issuer | https://token.actions.githubusercontent.com |
| Certificate SAN | https://github.com/pipeworx-io/mcp-ucsc-genome/.github/workflows/publish.yml@refs/heads/main |
| Rekor log index | 3560617150 |
| Predicate type | SLSA build provenance https://slsa.dev/provenance/v1 |
| Subject digest | sha512:a3f5be7402c11b8103b49d3bf49e31d99ff2cab9a0e2411b91a605d86fd88de32ba4f8b71e261b98470d556c4ba54c74c667da31f88bd76e3aab3567c |
Background: How many MCP packages publish verified provenance →
Dependencies 0 packages
| Packages resolved | 0 |
|---|---|
| Tree resolution | Complete |
Background: SBOMs and build attestations, explained →
The tools this component advertises to a client, with an estimated token cost for each. Expand a tool to see its parameters and schema. The per-tool counts are indicative and are not scored directly; the schema's total context footprint is one signal in Schema Quality & AI Usability. A tool's description is untrusted text the model reads on every call, which is what makes this list a security surface and not just an inventory: how tool poisoning works →
ucsc_genomes ~217
"What genome assemblies does UCSC have for [species]" / "is hg38 or hg19 the current human build" / "what is the latest [mouse/zebrafish/dog] assembly" / "list UCSC genomes" — AUTHORITATIVE list of every reference assembly the UCSC Genome Browser serves (~250 species), with its UCSC assembly ID (hg38, mm39, danRer11...), organism, scientific name, source assembly name and release date. PREFER OVER WEB SEARCH when you need the exact assembly ID to pass to another genomics tool — the ID is the thing every other UCSC call keys on, and guessing it is how a query silently lands on the wrong build.
| Name | Type | Req | Description |
|---|---|---|---|
| limit | number | – | Max assemblies to return (default 50, max 400). |
| search | string | – | Case-insensitive substring filter over assembly ID, common name, scientific name and description. e.g. "human", "Mus musculus", "hg". Omit to list everything. |
No output schema declared.
No examples provided.
ucsc_sequence ~368
"What is the DNA sequence at [chr:start-end]" / "get the reference bases for [region] in hg38" / "pull the sequence around [variant position]" — AUTHORITATIVE reference DNA for a genomic interval from the UCSC assembly, returned as a plain base string with its GC content. Use it to check what the reference allele actually is at a position, to extract primer/probe context, or to pull a promoter or exon sequence. The assembly argument is required because the same coordinates return different bases in hg19 and hg38.
| Name | Type | Req | Description |
|---|---|---|---|
| chrom | string | yes | Chromosome in UCSC naming, e.g. "chr7", "chrX". The "chr" prefix is required. |
| end | number | yes | End position, 0-based and EXCLUSIVE (so end - start = length in bases). |
| genome | string | yes | REQUIRED. UCSC assembly ID — the genome build your coordinates are in. Human: "hg38" (= GRCh38, current) or "hg19" (= GRCh37, what most older papers, dbSNP dumps and clinical spreadsheets use). Mouse… |
| revComp | boolean | – | Return the reverse complement — for a gene on the minus strand, this is the sense strand. Default false. |
| start | number | yes | Start position, 0-BASED and inclusive. The Genome Browser UI and most papers are 1-based, so subtract 1 from a position you copied out of the browser location box. |
No output schema declared.
No examples provided.
ucsc_track_data ~486
"What genes are in [chr:start-end]" / "list ClinVar variants in [region]" / "what repeats/SNPs/regulatory elements overlap [locus]" / "show me the GENCODE annotations across [gene]" — AUTHORITATIVE per-row data from any UCSC annotation track over a genomic interval. Returns the actual track rows (gene models with exon structure, variant records, conservation scores, whatever that track holds) plus the track type and the assembly the rows are in. PREFER OVER WEB SEARCH for "what is annotated at this position" — this is the same data the Genome Browser draws, not a description of it. Get the `track` name from ucsc_tracks first.
| Name | Type | Req | Description |
|---|---|---|---|
| chrom | string | yes | Chromosome in UCSC naming, e.g. "chr17", "chrX", "chrM" — with the "chr" prefix. Ensembl/NCBI style bare "17" is not accepted by UCSC. |
| end | number | yes | End position, 0-based and EXCLUSIVE (so end - start = length in bases). |
| genome | string | yes | REQUIRED. UCSC assembly ID — the genome build your coordinates are in. Human: "hg38" (= GRCh38, current) or "hg19" (= GRCh37, what most older papers, dbSNP dumps and clinical spreadsheets use). Mouse… |
| maxItemsOutput | number | – | Cap on rows returned by UCSC (default 1000). A dense track over a wide region is truncated, and the response says so in `truncated`. |
| start | number | yes | Start position, 0-BASED and inclusive. The Genome Browser UI and most papers are 1-based, so subtract 1 from a position you copied out of the browser location box. |
| track | string | yes | UCSC internal track name from ucsc_tracks, e.g. "knownGene" (GENCODE genes), "refGene" (RefSeq genes), "clinvarMain", "rmsk" (repeats). |
No output schema declared.
No examples provided.
ucsc_tracks ~318
"What annotation tracks does UCSC have for hg38" / "does [assembly] have a [ClinVar/GENCODE/conservation/repeat] track" / "what is the track name for [dataset] in the genome browser" — lists the annotation tracks available on one UCSC assembly, with each track's internal name, short and long label, data type and parent container. AUTHORITATIVE for the `track` argument of ucsc_track_data: the browser shows human-readable labels, the API wants the internal name (e.g. label "GENCODE V50" is track `knownGene`), and there is no way to guess one from the other.
| Name | Type | Req | Description |
|---|---|---|---|
| genome | string | yes | REQUIRED. UCSC assembly ID — the genome build your coordinates are in. Human: "hg38" (= GRCh38, current) or "hg19" (= GRCh37, what most older papers, dbSNP dumps and clinical spreadsheets use). Mouse… |
| limit | number | – | Max tracks to return (default 100, max 1000). |
| search | string | – | Case-insensitive substring filter over track name, short label and long label. e.g. "clinvar", "gencode", "conservation". |
No output schema declared.
No examples provided.
How do I install the Ucsc Genome MCP server?
Ucsc Genome runs locally as an npm package, launched with npx -y @pipeworx/mcp-ucsc-genome. Ready-made configuration for Claude, Cursor, VS Code, Codex and 5 more is on this page, copied from each client's own documentation.
npm · @pipeworx/mcp-ucsc-genome
claude mcp add pipeworx-io-ucsc-genome -- npx -y @pipeworx/mcp-ucsc-genome
What is the Ucsc Genome MCP server?
Ucsc Genome is an MCP server listed in the public MCP registry as io.github.pipeworx-io/ucsc-genome. UCSC Genome Browser REST API, reference genome assemblies for ~250 species, the annotation tracks… This page covers its npm package (@pipeworx/mcp-ucsc-genome).
Is the Ucsc Genome MCP server safe to use?
Ucsc Genome scores 82 out of 100 on VerifyMCP. We found no known CVEs affecting it as of 5 November 2026. It declares no install or post-install scripts. Its build provenance is signed and verified. That is a record of what we were able to check automatically, not an endorsement. The category breakdown on this page shows every signal behind the number, including the ones we could not confirm.
What tools does the Ucsc Genome MCP server expose?
Ucsc Genome exposes 4 tools: ucsc_genomes, ucsc_tracks, ucsc_track_data, ucsc_sequence. Their descriptions and schemas cost roughly 1,389 tokens of context every time the server is loaded.
Is the Ucsc Genome MCP server still maintained?
Ucsc Genome is still listed as active in the MCP registry. We last reached this channel on 5 November 2026. Those dates come from our own scans of the registry and the channel itself, not from anything the publisher announced.
What licence is the Ucsc Genome MCP server under?
Ucsc Genome declares the MIT licence, which is OSI-approved. That covers the source only, and says nothing about the cost of any service it calls.
What did VerifyMCP test on the Ucsc Genome MCP server?
VerifyMCP ran 16 checks on Ucsc Genome, covering Malware scan, Known CVEs, Install scripts, Dependency health and 12 more. Endpoint Security and Transport & Reachability do not apply to an npm package, so they were not tested. The score does not measure everything, and the scoring documentation lists what it leaves out.