Genome Sequence for a Chromosome Region (UCSC Genome Browser)

ucscgenome/genome-sequence

Returns the reference DNA sequence of a region of a UCSC Genome Browser genome assembly (for example hg38 for human or mm39 for mouse), given the chromosome and the start and end coordinates, optionally as the reverse complement. Lowercase letters mark soft-masked repeats. The response is as long as the region, one base per character, so ask for the region you need and not a whole chromosome. Calls are throttled to one every 15 seconds across all customers. UCSC asks users of the Genome Browser to cite its publications. Data from the UCSC Genome Browser, served by Eden Engine; not an official UCSC product.

activeper callv1

Price

$0.0026 per call

You pay the price shown. If a call turns out to cost more than its quote, you pay the actual price, capped at twice the quote. No monthly minimum. Top-ups start at $5.

Data source

UCSC Genome Browser (University of California, Santa Cruz)

Data from the UCSC Genome Browser, University of California, Santa Cruz (genome.ucsc.edu/license/). No attribution is required by the licence; UCSC asks that users cite its publications. Served by Eden Engine; not an official UCSC product.

Use it

Five steps: search, inspect, learn, run, settle. No per-tool setup; your agent reaches this tool through the meta-tools it already has.

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agent

// 1. search: find the tool
omnial_search({ query: "what you need" })

// 2. inspect: price and input schema
omnial_inspect({ tool: "ucscgenome/genome-sequence" })

// 3. learn: read the usage guide at runtime
omnial_learn({ tool: "ucscgenome/genome-sequence" })

// 4. run: price the exact call first, then run it
omnial_execute({ tool: "ucscgenome/genome-sequence", input: { /* see input_schema */ }, dry_run: true })
omnial_execute({ tool: "ucscgenome/genome-sequence", input: { /* ... */ } })

// 5. settle: the call is charged when it finishes, nothing to do

Not connected yet? Point your MCP client at https://mcp.eden-engine.com/mcp, then copy a config for your client.

Pricing

Every charge this tool can incur.

Charge	Price
Per call	$0.0026

Updated: Oct 20, 2026

Input and output schemas

Input schema

input_schema.json

{
  "type": "object",
  "required": [
    "genome",
    "chrom",
    "start",
    "end"
  ],
  "properties": {
    "end": {
      "type": "integer",
      "minimum": 1,
      "description": "End position of the region, 1-based and after start, for example 5678. The region has end minus start bases; the response is one character per base, so keep the region small."
    },
    "chrom": {
      "type": "string",
      "pattern": "^[A-Za-z0-9_.]{1,64}$",
      "description": "The chromosome or sequence name in that assembly, for example chr1, chrX or chrM."
    },
    "start": {
      "type": "integer",
      "minimum": 0,
      "description": "Start position of the region, 0-based, for example 4321."
    },
    "genome": {
      "type": "string",
      "pattern": "^[A-Za-z0-9_.]{1,64}$",
      "description": "The UCSC genome assembly name, for example hg38 (human), hg19 or mm39 (mouse)."
    },
    "rev_comp": {
      "enum": [
        1
      ],
      "type": "integer",
      "description": "Set to 1 to return the reverse complement of the region. Leave out for the forward strand."
    }
  },
  "additionalProperties": false
}

Output schema

output_schema.json

{
  "type": "object",
  "required": [
    "genome",
    "chrom",
    "start",
    "end",
    "dna"
  ],
  "properties": {
    "dna": {
      "type": "string",
      "description": "The sequence of the region. Lowercase letters are soft-masked repeats; uppercase are not."
    },
    "end": {
      "type": "integer",
      "description": "End of the region, as sent."
    },
    "chrom": {
      "type": "string",
      "description": "The chromosome that was queried."
    },
    "start": {
      "type": "integer",
      "description": "Start of the region, as sent."
    },
    "genome": {
      "type": "string",
      "description": "The assembly name that was queried."
    },
    "downloadTime": {
      "type": "string",
      "description": "When UCSC served the request, in a non-standard format such as 2026:10:20T00:13:08Z."
    },
    "downloadTimeStamp": {
      "type": "integer",
      "description": "The same instant as Unix seconds. Prefer this to downloadTime."
    }
  },
  "description": "The requested region as the UCSC API returns it.",
  "additionalProperties": true
}