ImmunoGraph MCP

validate_sequence

Read-onlyIdempotent

Validate a single protein FASTA record and get its normalized sequence, length, header, and SHA-256 identity before peptide generation or prediction; invalid input returns a structured error.

Instructions

Validate one protein FASTA record and return its normalized sequence, length, header, and SHA-256 identity. Use before peptide generation or prediction; this checks sequence syntax, not structure or biological activity. Invalid input returns a structured validation error.

Input Schema

Name	Required	Description	Default
`fasta`	Yes	One protein FASTA record with header and amino-acid sequence.
`profileVersion`	Yes	Version of the sequence validation profile; mvp-v1.0 is the current profile.

Output Schema

Name	Required	Description
`ok`	Yes	Whether execution completed successfully.
`data`	No	Tool-specific result fields on success.
`meta`	Yes	Run identifiers, timings, and input/output hashes.
`error`	No	Structured failure on unsuccessful execution.

Schema Changelog

Changes observed during successful MCP inspections.

Changed3 schema fields changedv0.2.1Oct 31, 2026

addedInput schema / properties / fasta / description

Added value: +"One protein FASTA record with header and amino-acid sequence."

addedInput schema / properties / profileVersion / description

Added value: +"Version of the sequence validation profile; mvp-v1.0 is the current profile."

changedOutput schema / (root)

Previous value: -nullNew value: +{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "additionalProperties": {},
+  "properties": {
+    "data": {
+      "additionalProperties": {},
+      "description": "Tool-specific result fields on success.",
+      "properties": {},
+      "type": "object"
+    },
+    "error": {
+      "additionalProperties": false,
+      "description": "Structured failure on unsuccessful execution.",
+      "properties": {
+        "category": {
+          "type": "string"
+        },
+        "code": {
+          "type": "string"
+        },
+        "details": {
+          "additionalProperties": {},
+          "properties": {},
+          "type": "object"
+        },
+        "message": {
+          "type": "string"
+        },
+        "retryable": {
+          "type": "boolean"
+        }
+      },
+      "required": [
+        "code",
+        "category",
+        "message",
+        "retryable"
+      ],
+      "type": "object"
+    },
+    "meta": {
+      "additionalProperties": {},
+      "description": "Run identifiers, timings, and input/output hashes.",
+      "properties": {
+        "completedAt": {
+          "type": "string"
+        },
+        "durationMs": {
+          "type": "number"
+        },
+        "inputHash": {
+          "type": "string"
+        },
+        "outputHash": {
+          "type": "string"
+        },
+        "requestId": {
+          "type": "string"
+        },
+        "runId": {
+          "type": "string"
+        },
+        "startedAt": {
+          "type": "string"
+        },
+        "toolName": {
+          "type": "string"
+        },
+        "toolVersion": {
+          "type": "string"
+        }
+      },
+      "required": [
+        "requestId",
+        "runId",
+        "toolName",
+        "toolVersion",
+        "startedAt",
+        "inputHash"
+      ],
+      "type": "object"
+    },
+    "ok": {
+      "description": "Whether execution completed successfully.",
+      "type": "boolean"
+    }
+  },
+  "required": [
+    "ok",
+    "meta"
+  ],
+  "type": "object"
+}

First observedv0.2.0Oct 31, 2026

TDQS

A4.3/5.0

Behavior4/5

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

Annotations already declare readOnlyHint and idempotentHint, so the safety profile is covered. The description adds real value beyond that: it discloses what is returned (normalized sequence plus a SHA-256 identity) and how failures behave ('invalid input returns a structured validation error'), rather than throwing. Minor gap: no statement about whether normalization ever mutates/rejects residues.

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?

Three short sentences, front-loaded with the action and returns, followed by the when-to-use and the failure mode. No filler or restated title.

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 two-parameter, read-only validation tool with an existing output schema and full schema coverage, the description supplies everything needed: input shape, when to call it, what it does not check, and error behavior.

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 description coverage is 100%, so both 'fasta' and 'profileVersion' are already documented in the schema. The description reinforces the single-record constraint ('one protein FASTA record') but says nothing about profileVersion or the significance of profile selection, so it adds little beyond structured data.

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 a specific verb and scope ('Validate one protein FASTA record') and enumerates what is produced (normalized sequence, length, header, SHA-256 identity). This clearly separates it from siblings like validate_structure, validate_thresholds, or validate_compound.

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?

Gives an explicit lifecycle position ('Use before peptide generation or prediction') and an explicit scope exclusion ('checks sequence syntax, not structure or biological activity'), which implicitly routes structural checks elsewhere. It does not name the sibling tool (validate_structure) directly, so it stops short of a full 5.

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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