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get_fasta

Retrieve raw FASTA sequences for one or more UniProtKB accessions, with silent handling of unknown accessions and strict validation for malformed entries.

Instructions

Return raw FASTA sequence(s) for one or more UniProtKB accessions.

A single accession uses the entry endpoint; a list uses the batch /accessions endpoint. Well-formed but unknown/obsolete accessions are dropped silently (a note reports the count discrepancy), but a malformed-format accession makes UniProt reject the whole request — so pass syntactically valid accessions.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
accessionsYesOne accession (string) or several (list of strings), e.g. ['P38398', 'P04637'].

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior5/5

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

Discloses important behaviors: endpoint selection (single vs batch), silent dropping of unknown/obsolete accessions with a note, and rejection of malformed accessions. No annotations exist, so description carries full transparency burden and does so thoroughly.

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?

Three sentences efficiently cover purpose, endpoint behavior, and critical warnings. No fluff, well-structured.

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?

For a simple one-parameter tool, the description covers all essential aspects: what it returns, how it handles different inputs, and error cases. Output schema exists and need not be explained.

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 the parameter fully, but the description adds significant meaning: the endpoint logic conditional on input size and the consequences of different accession types. This goes beyond the schema description.

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 tool returns raw FASTA sequences for UniProtKB accessions. It distinguishes from siblings like get_entry by specifying the output format, and the verb is specific.

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?

Context for when to use is clear (requesting FASTA), but no explicit comparison to siblings like get_entry or map_ids. However, the description provides critical usage notes about accessions, which guide correct invocation.

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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