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genbank_get

Read-only

Retrieve GenBank/RefSeq nucleotide sequences as GenBank or FASTA text by accession; optionally slice a base-pair region to obtain full sequences when a record exceeds size limits.

Instructions

Fetch a GenBank/RefSeq nucleotide record as text (GenBank flat file or FASTA).

Whole-record fetches are capped at 2,000,000 bp — larger records require a seq_start/seq_stop region (1-based, inclusive, up to 10 Mb span; set strand=2 for a reverse-strand slice where seq_start > seq_stop — the region field echoes the request as given, while NCBI's text shows complement(min..max)). Output guard: sequence_text is truncated to its first 200,000 characters when oversized — request a narrower region for the full text.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
formatNoRecord format: genbank flat file (default) or fastagenbank
strandNoStrand: 1=plus (default), 2=minus (reverse slice; allows seq_start > seq_stop)
seq_stopNoRegion stop (1-based, inclusive)
accessionYesGenBank/RefSeq accession, versioned or bare — NC_000023.11, NG_017013.2, KJ668569.2
seq_startNoRegion start (1-based, inclusive) — required with seq_stop for records over 2 Mb
max_response_bytesNoHard cap on the raw NCBI response in characters (default 30,000,000) — oversized responses error instead of truncating
Install Server

TDQS

A4.6/5.0
Behavior5/5

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

The annotations provide readOnlyHint and openWorldHint, and the description adds substantial operational detail beyond those: the 2,000,000 bp cap, 10 Mb region span, reverse-strand semantics, region echo behavior, NCBI complement notation, 200,000-character truncation, and the max_response_bytes error behavior. There is no contradiction with the read-only annotation.

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 first sentence gives a crisp purpose statement, and the second paragraph packs multiple complex rules into compact prose with no filler. Every sentence contributes to correct invocation, and the most important scope-limiting facts appear early.

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 covers every edge case that could cause a failed or misleading call: record-size caps, region span limits, strand semantics, truncation behavior, and the max_response_bytes hard cap. Since there is no output schema, the description's detail about the returned text and its truncation behavior is especially valuable for an agent deciding whether a request will succeed.

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

Parameters5/5

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

The schema covers all six parameters with 100% description coverage, and the description goes well beyond it by explaining 1-based inclusive coordinates, the cap that makes seq_start/seq_stop required, the strand=2 reverse-slice usage, and the truncation guard that motivates max_response_bytes. This transforms the parameter names into actionable invocation knowledge.

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 opening sentence, 'Fetch a GenBank/RefSeq nucleotide record as text (GenBank flat file or FASTA)', names a specific verb, a precise resource, and the output formats. This clearly distinguishes genbank_get from genbank_search, which is about discovery, and from genbank_genes, which targets gene records rather than nucleotide records.

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?

The description gives detailed operational conditions: whole-record fetches are capped at 2,000,000 bp, larger records require seq_start/seq_stop, and strand=2 is needed for reverse-strand slices. However, it does not explicitly state when to choose this tool over alternatives such as genbank_search, gene_get, or ensembl_region; that guidance is implied by the tool name rather than stated.

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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