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RNAcentral MCP Server

RNAcentral MCP Server

Official
by RNAcentral

export_sequences

Retrieve bulk RNA sequences by query and filters in FASTA or Parquet format for large-scale uses such as ML dataset generation.

Instructions

Export bulk RNA sequences matching a query in FASTA or Parquet format. Use this for large-scale data retrieval (e.g., ML dataset generation).

Args: query: Search term (e.g., "telomerase", "hsa-mir-126", "HOTAIR") rna_type: Filter by RNA type (e.g., "miRNA", "lncRNA", "tRNA") taxon: Taxon name or NCBI Taxonomy ID. expert_db: Source database (e.g., "miRBase", "GENCODE", "Ensembl") has_secondary_structure: Filter for RNAs with known 2D structure min_length: Minimum sequence length (nt) max_length: Maximum sequence length (nt) format: Output format ("fasta" or "parquet", default "fasta")

Input Schema

NameRequiredDescriptionDefault
queryYes
taxonNo
formatNofasta
rna_typeNo
expert_dbNo
max_lengthNo
min_lengthNo
has_secondary_structureNo

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.2.1

TDQS

A3.6/5.0
Behavior3/5

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

No annotations exist, so the description carries the full burden, and it does disclose the bulk/export nature and both output encodings. It says nothing about result-size limits, truncation or streaming behavior, whether 'export' produces a file path versus inline payload, or any permission requirements — meaningful gaps for a bulk retrieval tool. Annotations are absent but an output schema exists, which softens the return-value 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?

Front-loaded with purpose and usage in two sentences, then a compact per-parameter list; every line adds information. The Args block restates parameter names already present in the schema, a minor redundancy, but the grouping is scannable and waste-free.

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?

With 8 parameters, zero annotation coverage, and only one required field, the description gives an agent enough to construct a call: purpose, scale-oriented usage, and an example-bearing description for every parameter. Return values are covered by the output schema, so the remaining gap is behavioral (size limits, query syntax) rather than structural.

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 description coverage is 0%, and the description compensates by documenting all eight parameters with concrete examples ('telomerase', 'hsa-mir-126', 'HOTAIR'; 'miRBase', 'GENCODE', 'Ensembl') and units for the length bounds. It falls short on the most important parameter — the query's syntax/matching semantics (free text, exact ID, boolean?) are not specified, nor are the allowed values for format constrained beyond an example.

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 specific verb and resource ('Export bulk RNA sequences matching a query') plus the output formats, which is far more than a tautology. It does not name the sibling it differs from (search_sequence, query_rnacentral), so an agent must infer the boundary itself, keeping it 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 Guidelines3/5

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

'Use this for large-scale data retrieval (e.g., ML dataset generation)' gives a real usage cue that implicitly contrasts with the single-record search siblings. However it never names an alternative tool or states when NOT to use it (e.g., for a single sequence lookup use search_sequence), leaving the routing decision to inference.

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