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search_uniref

Search UniRef clusters (sequence-similarity groups at 100/90/50% identity) by query. Returns cluster ID, name, member counts, and representative member.

Instructions

Search UniRef clusters (sequence-similarity clusters of UniProt proteins).

UniRef100/90/50 group sequences at 100/90/50% identity. Returns cluster id, name, member/organism counts, and the representative member. Use identity to restrict to one clustering level.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
queryYesUniRef query, e.g. 'BRCA1', 'uniprotkb:P38398', or 'taxonomy_id:9606'.
identityNoCluster identity threshold: '1.0'=UniRef100, '0.9'=UniRef90, '0.5'=UniRef50.
sizeNoMax clusters to return (1-500).
formatNo'summary' = compact list (default); 'tsv' = table.summary

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior4/5

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

The description discloses return fields (cluster id, name, counts, representative) and the effect of the identity parameter, providing sufficient transparency for a read-only search tool without annotations.

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

Conciseness4/5

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

The description is concise with three sentences, front-loaded with key information, and free of fluff, though it could be slightly more streamlined.

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?

Given the output schema exists, the description adequately covers what the tool does and what it returns, making it complete for a search tool.

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% and descriptions are clear; the overall description adds background context but does not significantly enhance parameter understanding beyond the schema.

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 it searches UniRef clusters, distinguishes it from sibling tools like search_uniprotkb and get_entry by specifying the database and the nature of clusters.

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 query examples and mentions the identity parameter, but does not explicitly state when to use this tool over alternatives or provide exclusion criteria.

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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