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ncbi_fetch_sequence

Retrieve FASTA sequences from NCBI by accession, gene symbol, or keyword. Select nucleotide, gene, or protein database for reference sequences in downstream analysis.

Instructions

Download nucleotide/protein sequences (FASTA) from NCBI. 从 NCBI 下载核酸/蛋白序列(FASTA),支持 accession、gene symbol、关键词。DB options: nucleotide/gene/protein. 数据库可选 nucleotide/gene/protein,for getting reference sequences for downstream analysis. 用于获取参考序列做下游分析。

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
dbNonucleotide
queryYes
max_idsNo
rettypeNofasta

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior3/5

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

No annotations are provided, so the description carries the full burden. It does disclose the core behavior: downloading FASTA sequences and supporting accession/gene symbol/keyword queries, with selectable databases. However, it omits details such as result count limits, rate limits, or what happens for ambiguous queries across the different database options.

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

Conciseness2/5

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

The description is front-loaded with the key action, but it repeats nearly every statement in both English and Chinese, adding redundant text without additional information. This bilingual duplication makes it less concise than it should be for an AI agent consuming the definition.

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

Completeness2/5

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

An output schema exists, so return-value documentation is not required, but the tool is otherwise under-specified. The description does not explain max_ids behavior, rettype semantics, or provide when-to-use guidance relative to sibling tools. An agent would still need to infer or probe several invocation details.

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

Parameters2/5

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

Schema description coverage is 0%, so the description must compensate. It partially explains 'query' (supports accession, gene symbol, keyword) and 'db' (nucleotide/gene/protein), but it does not explain 'max_ids' or 'rettype'. An agent cannot fully understand the effect of changing these parameters from the description alone.

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 clearly states the action ('Download'), the resource ('nucleotide/protein sequences (FASTA) from NCBI'), and the supported query types. It is distinct enough from siblings like pubmed_search or blast_search because it uniquely identifies NCBI sequence retrieval with FASTA output.

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 contextual purpose ('for getting reference sequences for downstream analysis') and mentions database options, but it does not explicitly state when to use this tool versus alternatives like ENA sequence search or BLAST. There are no exclusion criteria or alternative tool references.

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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