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musharna

plant-genomics-mcp

find_homologs_synth

Searches for homologous sequences using BLAST and adds UniProt annotations to each result, delivering ranked homologs with comprehensive records.

Instructions

Synthesis: one-call equivalent of the find_homologs prompt. Runs BLAST then resolves UniProt-shaped subject accessions via the batch UniProt helper. Returns ranked hits each annotated with their UniProt record (or null if subject_id is not a UniProt accession).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
sequenceYesQuery sequence (protein or nucleotide)
programNoblastp
top_nNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
toolYesSynthesis tool name, e.g. analyze_locus_synth
inputYesEchoed input arguments
started_atYesISO 8601 UTC timestamp
elapsed_sYesTotal orchestrator wall time
stepsYesPer-backend execution rows
resultNoComposed cross-source result; None if root step failed
Behavior4/5

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

With no annotations provided, the description carries the full burden. It transparently describes the two-step process (BLAST then resolution) and clarifies that results include UniProt records or null for non-UniProt accessions. This is sufficient for a read-only search tool, though it does not mention auth or rate limits.

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?

Two sentences front-load the purpose ('one-call equivalent') and process. Every phrase earns its place: no redundancy, no fluff. The structure is ideal for quick parsing by an AI agent.

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 complexity (3 parameters, output schema exists), the description covers the core workflow and return behavior. The output schema handles structured details. Minor gaps: does not mention program defaults or top_n limits, but the schema covers those. Overall adequate for a synthesized tool.

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 coverage is low (33%): only 'sequence' has a description. The description does not add meaning beyond the schema for 'program' (enum) or 'top_n' (integer with defaults). It fails to compensate for the undocumented parameters, leaving the agent with gaps.

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 is a 'one-call equivalent of the find_homologs prompt' that runs BLAST then resolves UniProt accessions. This distinguishes it from sibling tools like blast_sequence (which only does BLAST) or resolve_locus_to_uniprot (which only resolves). The verb 'runs' and specific resource naming make the purpose explicit.

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 implies this tool replaces a multi-step prompt, but does not explicitly state when to use it over alternatives like running blast_sequence followed by resolve_locus_to_uniprot. No exclusions or specific context are provided, leaving the agent to infer usage.

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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