protein-tools-mcp

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detect_sequence_type

Classify a FASTA sequence as protein, DNA, RNA, ambiguous, or unknown from a file path or raw text, returning confidence and detailed notes.

Instructions

Detect whether a FASTA sequence is protein, DNA, RNA, ambiguous, or unknown.

Accepts a FASTA file path (is_file=True) or raw FASTA text (is_file=False). Returns the type classification with confidence and detailed notes.

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "source": "<source>"
    },
    "name": "detect_sequence_type"
  }
}

Input Schema

Name	Required	Description	Default
`source`	Yes
`is_file`	No
`sequence_index`	No

Output Schema

Name	Required	Description	Default
`result`	Yes

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.0Oct 20, 2026

TDQS

A3.8/5.0

Behavior3/5

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

No annotations are provided, so the description carries the full burden. It usefully discloses the dual input modes (is_file=True/False) and that output includes confidence and notes, but says nothing about limitations such as behavior on multi-sequence input, how sequence_index affects selection, or error handling.

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, front-loaded sentences with zero filler: purpose first, then input modes, then return content. Every sentence earns its place.

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

Completeness4/5

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

An output schema exists, so return values needn't be re-explained, and the description correctly focuses on inputs and the classification categories. It is nearly complete, with only sequence_index semantics and multi-sequence handling left unaddressed.

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 0%, so the description must compensate. It clarifies the source/is_file relationship well, but the sequence_index parameter (default 0) is never mentioned, leaving one of three parameters semantically unexplained.

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 ('Detect') and resource ('FASTA sequence') and enumerates the exact classification outputs (protein, DNA, RNA, ambiguous, unknown). This clearly distinguishes it from siblings like read_fasta, fasta_stats, and aa_composition, which read or summarize rather than classify type.

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

Usage Guidelines3/5

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

The description explains the two input modes (file path vs raw text via is_file), which implies how to invoke it, but gives no explicit when-to-use guidance versus alternatives like read_fasta or fasta_stats. Usage context is implied rather than stated.

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