protein-tools-mcp

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fasta_stats

Summarize multi-FASTA inputs with N50, length statistics, per-type counts, and DNA GC%, providing clear metrics for sequence dataset assessment.

Instructions

Multi-FASTA summary: N50, length stats, per-type counts, GC%.

GC% is computed over DNA records only (null with a note when none). Free; local compute.

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": "fasta_stats"
  }
}

Input Schema

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

Output Schema

Name	Required	Description	Default
`result`	Yes

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.0Oct 20, 2026

TDQS

B3.2/5.0

Behavior3/5

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

With no annotations, the description carries the full burden. It usefully discloses one real edge behavior — GC% is restricted to DNA records and returns null with a note otherwise — plus the zero-cost local execution profile. It says nothing about error handling for a missing/unreadable source or how the tool behaves on mixed or non-sequence input, leaving meaningful behavioral gaps.

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

Conciseness4/5

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

Three tight lines with the most important information (the metric set) front-loaded and no filler. The trailing fragments ('Free; local compute.') are information-dense rather than wasteful, though their telegraphic style is slightly abrupt.

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, so return values need not be explained. But for a 2-parameter tool with zero schema coverage and no annotations, the description omits how 'source' and 'is_file' interact, which is the main thing an agent needs to call it correctly.

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 coverage is 0%: the two parameters ('source', 'is_file') have only titles and a default, no descriptions. The description does not mention either parameter, so it fails to clarify the critical distinction between source-as-path versus source-as-inline-sequence implied by is_file=true.

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 names the resource (multi-FASTA) and enumerates the exact outputs (N50, length stats, per-type counts, GC%), which makes it unmistakable against siblings like read_fasta or aa_composition. However, it never explicitly contrasts itself with those siblings, which is the bar for a 5.

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?

Usage is only implied — an agent infers 'call this to summarize a FASTA file.' The 'Free; local compute' note gives a useful cost/local-vs-server signal for tool choice, but there is no statement of when to prefer this over alternatives (e.g. read_fasta, detect_sequence_type) or any exclusion.

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