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Get Genomic Sequence for Region

science.ensembl.sequence_region
Read-onlyIdempotent

Retrieve the raw DNA sequence for a genomic region (e.g. "17:7668402-7687550" on GRCh38). Returns the nucleotide sequence, molecule type, and sequence length. Useful for primer design, variant context, and comparative sequence analysis. Data: rest.ensembl.org (EMBL-EBI / Wellcome Sanger Institute), no auth required.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
regionYesGenomic region in "chromosome:start-end" format, GRCh38 coordinates (e.g. "X:1000000-1000100", "17:7668402-7687550" for TP53)
speciesYesSpecies name in Ensembl format — scientific snake_case (e.g. "homo_sapiens") or common alias (e.g. "human", "mouse")

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
errorNoPresent only when the call failed. Includes error code, message, request_id, and any provider-specific extras.
resultNoTool response payload. Shape varies per tool — consult the tool description and inputSchema. May be an object, array, string, or number depending on the upstream provider response.

Schema Changelog

Changes observed during successful MCP inspections.

  1. Added
  2. Removed
  3. Added
  4. Removed
  5. First observed

TDQS

A4.1/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare readOnlyHint, idempotentHint, and destructiveHint, so the safety profile is covered. The description adds valuable context beyond the annotations: the data source (rest.ensembl.org, EMBL-EBI / Wellcome Sanger Institute) and the fact that no auth is required, which informs the agent about prerequisites and origin of data.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is exceptionally concise: a single sentence for the action, one for return values, one for use cases, and one for data source/auth. Every sentence earns its place, and the key action is front-loaded.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a simple read-only tool with two well-documented parametersstant, full annotation coverage, and an output schema, the description covers everything an agent needs: what it returns, example input, source, and auth requirements. No critical gaps remain.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100% and both parameter descriptions are detailed including format and examples. The description's example region is redundant with the schema's example. The baseline of 3 is appropriate because the schema already handles parameter semantics; the description does not add meaningful information beyond the schema.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the action: 'Retrieve the raw DNA sequence for a genomic region' with a specific example and coordinates. It does not explicitly contrast with sibling tools like science.ensembl.gene_lookup, so it lacks the 'distinguishes from siblings' criterion for a 5, but it is far from vague.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description gives concrete use cases ('primer design, variant context, and comparative sequence analysis') which clarifies when to use it. It does not explicitly mention when not to use it or name alternative tools, but the context is clear enough for an agent to infer appropriate usage.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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