Skip to main content
Glama
RNAcentral MCP Server

RNAcentral MCP Server

Official
by RNAcentral

query_rnacentral

Search RNAcentral for RNA sequences by query, RNA type, taxonomy, source database, or secondary structure presence, and retrieve detailed metadata including Rfam, GO, and 2D structure annotations.

Instructions

Comprehensive search for RNA sequences using EBI Search and RNAcentral APIs. Combines text search filters with detailed metadata (Rfam, GO, 2D structure).

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. Prefer scientific names (e.g. "Homo sapiens", "Mus musculus") over common names if available. expert_db: Source database (e.g., "miRBase", "GENCODE", "Ensembl") has_secondary_structure: Filter for RNAs with known 2D structure limit: Number of results to return (default 10, max 20)

Input Schema

NameRequiredDescriptionDefault
limitNo
queryYes
taxonNo
rna_typeNo
expert_dbNo
has_secondary_structureNo

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.2.1

TDQS

B3.4/5.0
Behavior2/5

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

No annotations are provided, so the description carries the full behavioral burden. It discloses that results merge text-search hits with metadata sources (Rfam, GO, 2D structure) and that limit is capped at 20, but says nothing about result ranking, pagination, whether results are deduplicated, or error behavior — significant gaps for a six-parameter search tool with zero annotation coverage.

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 summary sentence followed by a compact per-argument block; each line adds information and there is no filler. Slightly verbose in restating parameter titles, but the structure is easy to scan.

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 need not be described, and all six parameters are documented despite 0% schema coverage. The remaining gap is the absence of any routing guidance relative to the several similar sibling search tools.

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%, so the description must do all the work, and it largely does: every parameter is explained with examples, taxon guidance recommends scientific names over common names, and the limit cap of 20 is added beyond the schema's bare default of 10. Only rna_type and expert_db lack enumerated accepted values.

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 ('Comprehensive search for RNA sequences') and names the data sources (EBI Search, RNAcentral) plus the metadata dimensions returned (Rfam, GO, 2D structure). It does not explicitly distinguish itself from siblings like search_sequence or get_rna_description, so an agent must infer the boundary.

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 by the phrase 'Comprehensive search' and the example query terms; there is no explicit when-to-use versus when-to-use-a-sibling guidance, no stated prerequisites, and no note on when the optional filters should be applied.

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