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genbank_search

Read-only

Search NCBI nucleotide records by gene name, accession, or field query to locate GenBank/RefSeq/INSDC sequences. Returns essential metadata such as length, organism, and topology for follow-up retrieval.

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

TableJSON 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")
Install Server

TDQS

A4.3/5.0
Behavior4/5

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

The annotations already declare the operation as read-only and open-world, so the safety profile is covered. The description adds useful behavioral context beyond that: it supports multiple query formats and enumerates the result fields (accession.version, definition, length_bp, organism, topology). This is especially valuable because there is no output schema.

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?

The description is compact and well-structured. The first sentence states the core purpose, the second provides query guidance and result details, and the final clause gives actionable chaining advice. No sentence is wasted.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

The description is complete enough for an agent to invoke the tool correctly. There is no output schema, but the description compensates by listing the returned fields. It also explains accepted query forms and suggests downstream uses, so the agent knows what to do with the results.

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?

The input schema already provides 100% parameter descriptions, so the baseline is 3. The description adds concrete query syntax examples and mentions result fields, but it does not add meaning to specific parameters beyond what the schema already states.

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 identifies a specific verb ('Search'), a specific resource (NCBI nucleotide records, explicitly GenBank/RefSeq/INSDC), and clearly distinguishes it from related tools by naming the nucleotide database. It also differentiates itself from sibling searches like gene_search and variant_search by stating its domain.

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?

The description tells the agent which query forms are accepted, including plain terms, accessions, and NCBI field syntax, with concrete examples. It also gives guidance on next steps by chaining accessions into genbank_get or genbank_genes, but it does not explicitly state when not to use this tool or name alternatives for exclusion.

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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