Genomics MCP

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get_sequence

Read-only

Retrieve reference sequence for a genomic interval from an indexed FASTA file. Specify contig, start, end, and assembly to get the exact bases.

Instructions

Reference sequence for an interval from an indexed FASTA. Available for: fasta.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`file`	Yes
`interval`	Yes

Output Schema

TableJSON Schema

Name	Required	Description	Default
`data`	No
`error`	No	Set when status is error.
`errors`	No	Per-source failures in partial results.
`limits`	No
`status`	Yes
`warnings`	No
`operation`	Yes
`provenance`	No
`truncation`	No
`source_status`	No
`schema_version`	No		1
`metadata_omitted`	No	Entries dropped from provenance/source_status/errors/warnings (or text shortened) to fit max_response_bytes. Absent when metadata is complete.

Schema Changelog

Changes observed during successful MCP inspections.

Changed1 schema field changedv0.1.1Sep 28, 2026

addedOutput schema / properties / metadata_omitted

Added value: +{
+  "anyOf": [
+    {
+      "additionalProperties": {
+        "type": "integer"
+      },
+      "type": "object"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "description": "Entries dropped from provenance/source_status/errors/warnings (or text shortened) to fit max_response_bytes. Absent when metadata is complete.",
+  "title": "Metadata Omitted"
+}

First observedv0.1.0Sep 24, 2026

TDQS

B3.4/5.0

Behavior3/5

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

Annotations already declare readOnlyHint=true and openWorldHint=true, so the safety profile is covered. The description adds that the operation targets an indexed FASTA and is available only for fasta, but it does not disclose error behavior, indexing prerequisites, auth considerations, or other operational traits. This is useful scoping context, not rich behavioral detail.

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?

Very short and front-loaded: the core retrieval purpose comes first, followed by the fasta availability note. No filler or redundant sentences; every fragment contributes to scoping the tool.

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

Completeness3/5

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

An output schema exists, and the nested input schema documents Interval and FileRef in detail, so return values and field constraints need not be repeated. However, the description is thin on when to choose this tool over sibling genomic tools and gives minimal invocation context, leaving clear gaps.

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

Parameters2/5

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

Schema description coverage is reported as 0%, so the description must compensate, but it does not document the file or interval parameters beyond the word 'interval' and 'indexed FASTA.' It omits required assembly, 0-based half-open coordinate semantics, contig naming, and file requirements such as index availability.

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?

States the specific resource returned: reference sequence for an interval from an indexed FASTA. 'Available for: fasta' scopes it to FASTA sources, distinguishing it from siblings like get_reads, get_variants, get_coverage, and get_features. An agent can identify this as sequence retrieval without opening the schema.

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

Usage Guidelines2/5

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

Only states availability for fasta; it gives no explicit guidance on when to use this tool versus alternatives like get_reads, get_coverage, or inspect_locus. No when-not conditions or routing cues are provided, leaving usage selection to inference.

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