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RNAcentral MCP Server

RNAcentral MCP Server

Official
by RNAcentral

get_secondary_structure_svg

Retrieve the secondary structure (2D diagram) of an RNA sequence as an SVG by providing its RNAcentral URS ID.

Instructions

Get the secondary structure (2D diagram) for an RNA sequence in SVG format.

Args: urs_id: The RNAcentral URS ID (e.g., 'URS0000049E57')

Input Schema

NameRequiredDescriptionDefault
urs_idYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.2.1

TDQS

B3.1/5.0
Behavior2/5

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

No annotations are supplied, so the description carries the full burden. It says the result is SVG but never clarifies whether that is raw SVG markup, a file/URL, or base64, nor what happens when no secondary structure exists (error, empty, fallback). For a no-annotation tool this is a real gap.

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?

Two short lines with the purpose front-loaded and no filler. The 'Args:' block slightly repeats the schema but is minimal and readable.

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?

For a one-parameter read tool with no annotations and no output schema, the description covers what the tool fetches but not the return shape or failure modes. An agent could call it, but not predict the response payload or handle the no-structure case.

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

Parameters4/5

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

Schema coverage is 0% and the schema only exposes a bare 'Urs Id' string, so the description is doing the work: it identifies the value as an RNAcentral URS ID and supplies a concrete example format ('URS0000049E57'). That is genuine added meaning beyond the schema, though it doesn't state whether the ID must already be mapped/canonical.

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?

States a concrete verb and resource — 'Get the secondary structure (2D diagram) for an RNA sequence' — plus the output format (SVG). It is clearly distinguishable from siblings like search_sequence and map_rna_id, though it never names an alternative explicitly, which keeps it just short of 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 Guidelines2/5

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

There is no when-to-use guidance, no mention of alternatives, and no stated preconditions such as whether the URS ID must correspond to a sequence with a known/predicted structure. The only usage signal is implicit in the purpose statement.

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