`ucsc_sequence`

Pack: ucsc-genome · Endpoint: https://gateway.pipeworx.io/ucsc-genome/mcp

No MCP client? Call it directly: GET https://gateway.pipeworx.io/v1/tools/ucsc_sequence for the schema, then POST the same URL with its arguments for the data.

“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.

Parameters

Name	Type	Required	Description
`genome`	string	yes
`chrom`	string	yes	Chromosome in UCSC naming, e.g. “chr7”, “chrX”. The “chr” prefix is required.
`start`	number	yes
`end`	number	yes
`revComp`	boolean	no	Return the reverse complement — for a gene on the minus strand, this is the sense strand. Default false.

Example call

Arguments

{
  "genome": "hg38",
  "chrom": "chr7",
  "start": 140753330,
  "end": 140753390
}

curl

curl -X POST https://gateway.pipeworx.io/ucsc-genome/mcp \
  -H 'Content-Type: application/json' \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/call","params":{"name":"ucsc_sequence","arguments":{"genome":"hg38","chrom":"chr7","start":140753330,"end":140753390}}}'

TypeScript (@pipeworx/sdk)

import { Pipeworx } from '@pipeworx/sdk';
const pipeworx = new Pipeworx();

const result = await pipeworx.call('ucsc_sequence', {
  "genome": "hg38",
  "chrom": "chr7",
  "start": 140753330,
  "end": 140753390
});

More examples

{
  "genome": "hg19",
  "chrom": "chr17",
  "start": 41276000,
  "end": 41276100,
  "revComp": true
}

Connect

Add this to your MCP client config, or use one-click install buttons:

{
  "mcpServers": {
    "ucsc-genome": {
      "url": "https://gateway.pipeworx.io/ucsc-genome/mcp"
    }
  }
}

See Getting Started for client-specific install steps.

ucsc_sequence