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Glama

Ensembl

by io.github.pipeworx-io

Sequence

sequence
Read-onlyIdempotent

"DNA / cDNA / CDS / protein sequence of [gene]" / "FASTA for [Ensembl ID]" / "get sequence of [transcript]" — sequence by Ensembl stable ID. Type defaults to "genomic"; pass "cdna", "cds", or "protein" for processed forms. Use for sequence retrieval in primer design, variant analysis, or downstream sequence tools.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
idYes
typeNogenomic (default) | cdna | cds | protein

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
idNoStable ID
seqNoDNA or protein sequence
query_typeNoQuery type (genomic/cdna/cds/protein)
molecule_typeNoMolecule type

Schema Changelog

Changes observed during successful MCP inspections. Dates show when Glama detected each change.

  1. Changed2 schema fields changed
    • addedInput schema / examples
      Added value: +[
+  {
+    "id": "ENSG00000157764"
+  },
+  {
+    "id": "ENST00000288602",
+    "type": "cdna"
+  }
+]
    • changedOutput schema / (root)
      Previous value: -nullNew value: +{
+  "description": "Sequence data for a stable ID",
+  "properties": {
+    "id": {
+      "description": "Stable ID",
+      "type": "string"
+    },
+    "molecule_type": {
+      "description": "Molecule type",
+      "type": "string"
+    },
+    "query_type": {
+      "description": "Query type (genomic/cdna/cds/protein)",
+      "type": "string"
+    },
+    "seq": {
+      "description": "DNA or protein sequence",
+      "type": "string"
+    }
+  },
+  "type": "object"
+}
  2. First observed

TDQS

A4.3/5.0
Behavior4/5

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

Beyond the readOnly/idempotent annotations, the description reveals that the type defaults to 'genomic' and that 'cdna', 'cds', or 'protein' must be passed for processed forms. This adds useful behavioral context not covered by annotations.

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?

The description is two sentences and front-loaded with examples. The first sentence is dense but efficient, noting the default type and alternatives. No wasted words, though structure could be slightly clearer.

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 annotations indicating a safe read operation and an output schema present, the description covers defaults, input types, and use cases. It is complete enough for straightforward sequence retrieval without over-explaining.

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?

The schema only describes the type parameter, leaving 'id' underdocumented. The description clarifies that 'id' is an Ensembl stable ID (gene or transcript) and explains the valid type values and default, effectively compensating for the 50% schema coverage.

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?

The description explicitly states the tool retrieves DNA/cDNA/CDS/protein sequences by Ensembl stable ID, with concrete example queries. This distinguishes it from sibling tools like lookup or variation, making its purpose unmistakable.

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

Usage Guidelines4/5

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

It provides clear use cases ('primer design, variant analysis, or downstream sequence tools') and explains the default type behavior. However, it does not explicitly mention alternatives or when not to use it, so it falls short of a 5.

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

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TDQS

A3.6/5.0
Disambiguation2/5

Multiple tool families heavily overlap: ask_pipeworx, ask_pipeworx_beta (explicitly identical), ask_pipeworx_grounded, deep_research, and validate_claim all answer natural-language questions, while polymarket_arbitrage, polymarket_edges, polymarket_edge_tracker, polymarket_fill_risk, polymarket_kalshi_spread, and bet_research all analyze prediction markets. An agent would struggle to pick the correct tool without reading very long descriptions.

Naming Consistency3/5

All names are snake_case and readable, but the style is inconsistent: some are bare nouns (sequence, variation, homology), some are single verbs (lookup, recall, forget), and others are long descriptive phrases (scan_competitor_ai_presence, polymarket_kalshi_spread). There is no consistent verb_noun or resource_noun pattern across the set.

Tool Count2/5

38 tools is excessive for a coherent server, and nearly all of them are unrelated to the server's stated name ('Ensembl') — only about 7 tools (lookup, lookup_symbol, sequence, variation, vep, xrefs, homology) actually belong to the Ensembl domain. The rest form several unrelated clusters (Pipeworx data queries, prediction markets, memory, subscriptions), making the tool count feel bloated and unfocused.

Completeness2/5

For an Ensembl server, the surface is thin: it covers ID lookup, sequence retrieval, variants, VEP, xrefs, and homology, but omits other core Ensembl functionality such as gene trees, alignments, regulation, expression, and assembly data. Meanwhile the many non-Ensembl tools don't form a complete domain of their own — they are a grab bag of unrelated utilities.

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