Skip to main content
Glama

genbank_search

Read-only

Search NCBI nucleotide records by gene, organism, accession, or field syntax to retrieve matching accessions, definitions, lengths, organisms, and topology for downstream sequence or gene lookup.

Instructions

Search NCBI nucleotide records (GenBank/RefSeq/INSDC).

Queries may be plain terms, an accession, or NCBI field syntax ("TP53[Gene Name] AND Homo sapiens[Organism]", "BRCA1[Gene Name]"). Results include accession.version, definition, length_bp, organism, and topology — chain accessions into genbank_get or genbank_genes.

Input Schema

NameRequiredDescriptionDefault
limitNoMaximum results
queryYesNucleotide query, e.g. "TP53[Gene Name] AND Homo sapiens[Organism]" or an accession
offsetNoResult offset for pagination
organismNoFilter by organism (e.g. "Homo sapiens")

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed2 schema fields changedv1.6.0-alpha.10
    • removedInput schema / additionalProperties
      Removed value: -false
    • addedInput schema / properties / offset / maximum
      Added value: +9007199254740991
  2. Changed1 schema field changedv1.6.0-alpha.1
    • addedInput schema / properties / query / minLength
      Added value: +1
  3. Addedv0.7.1

TDQS

A4/5.0
Behavior3/5

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

Annotations already declare readOnlyHint=true and openWorldHint=true, so the safety and external-corpus profile is covered. The description adds useful value by enumerating the returned fields (accession.version, definition, length_bp, organism, topology), but says nothing about result caps, pagination behavior, or rate limiting on an open-world NCBI endpoint.

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

Conciseness5/5

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

Two sentences, front-loaded with the resource and scope, then the query modes, then the return fields and handoff. No filler; every clause carries information an agent would act on.

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 no output schema, the description compensates by listing the fields returned, and it closes the loop on pagination-adjacent workflow by pointing to genbank_get/genbank_genes. It could be more complete by noting the default result limit of 10 or that offset pages through a possibly large hit count.

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

Parameters3/5

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

Schema coverage is 100%, so query, organism, limit, and offset are all documented in the schema itself, and the description's query-syntax examples largely duplicate the schema's own example. Baseline 3 is appropriate since the schema does the heavy lifting.

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?

States a specific verb+resource ('Search NCBI nucleotide records') and scopes the corpus explicitly (GenBank/RefSeq/INSDC). It also names the downstream siblings (genbank_get, genbank_genes), so an agent can distinguish this from gene_search, variant_search, and sra_search without opening schemas.

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?

Gives concrete query-form guidance (plain terms, accession, or field syntax with worked examples) plus a next-step routing hint to genbank_get/genbank_genes. It lacks explicit negative guidance — nothing says when to prefer sra_search or gene_search instead — 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.