Ensembl

Sequence

sequence

Read-onlyIdempotent

"DNA / cDNA / CDS / protein sequence of [gene]" / "FASTA for [Ensembl ID]" / "get sequence of [transcript]" — sequence by Ensembl stable ID. Type defaults to "genomic"; pass "cdna", "cds", or "protein" for processed forms. Use for sequence retrieval in primer design, variant analysis, or downstream sequence tools.

Example tool call

This call uses example arguments supplied in the tool’s input schema.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "id": "ENSG00000157764"
    },
    "name": "sequence"
  }
}

Input Schema

Name	Required	Description
`id`	Yes
`type`	No	genomic (default) \| cdna \| cds \| protein
`assembly`	No	Human genome build: "GRCh38" (the default) or "GRCh37" (= hg19). Coordinates you pass and coordinates you get back are both in this build. Older variant lists, spreadsheets and published tables are usually GRCh37.

Output Schema

Name	Required	Description
`id`	No	Stable ID
`seq`	No	DNA or protein sequence
`query_type`	No	Query type (genomic/cdna/cds/protein)
`molecule_type`	No	Molecule type

Schema Changelog

Changes observed during successful MCP inspections.

Changed1 schema field changedSep 7, 2026

addedInput schema / properties / assembly

Added value: +{
+  "description": "Human genome build: \"GRCh38\" (the default) or \"GRCh37\" (= hg19). Coordinates you pass and coordinates you get back are both in this build. Older variant lists, spreadsheets and published tables are usually GRCh37.",
+  "type": "string"
+}

Changed2 schema fields changedMay 27, 2026

addedInput schema / examples

Added value: +[
+  {
+    "id": "ENSG00000157764"
+  },
+  {
+    "id": "ENST00000288602",
+    "type": "cdna"
+  }
+]

changedOutput schema / (root)

Previous value: -nullNew value: +{
+  "description": "Sequence data for a stable ID",
+  "properties": {
+    "id": {
+      "description": "Stable ID",
+      "type": "string"
+    },
+    "molecule_type": {
+      "description": "Molecule type",
+      "type": "string"
+    },
+    "query_type": {
+      "description": "Query type (genomic/cdna/cds/protein)",
+      "type": "string"
+    },
+    "seq": {
+      "description": "DNA or protein sequence",
+      "type": "string"
+    }
+  },
+  "type": "object"
+}

First observedMay 16, 2026

TDQS

A4.6/5.0

Behavior4/5

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

Annotations already indicate read-only, idempotent, open-world, and non-destructive behavior. The description adds appropriate context by describing sequence retrieval and default behavior, and it contains no contradictions with the annotations.

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 concise and front-loaded, starting with what the tool returns and then clarifying options and use cases. No redundant or vague wording is present.

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?

The description covers the essential defaults, accepted type values, assembly behavior, and typical use cases. Since the tool has an output schema, the lack of a detailed return-value explanation is not a gap.

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

Parameters5/5

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

The description and schema together explain all parameters: id is an Ensembl stable ID, type lists the allowed values with the default, and assembly clarifies genome build options and coordinate implications. Examples reinforce the parameter usage.

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

Purpose5/5

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

The description clearly states the tool retrieves DNA, cDNA, CDS, or protein sequences by Ensembl stable ID, with explicit mention of FASTA output. It specifies the default type and supported type values, making the tool's purpose unambiguous.

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 such as primer design, variant analysis, and downstream sequence tools. It does not explicitly contrast this tool with sibling tools like homology, variation, or vep, but the use-case framing provides sufficient practical guidance.

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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