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musharna

plant-genomics-mcp

find_homologs_synth

Find homologous sequences by BLASTing a query protein or nucleotide and retrieving UniProt-annotated results.

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 full burden. It discloses that it runs BLAST, then resolves subject accessions via a batch helper, and returns null for non-UniProt accessions. This provides adequate behavioral context for a bioinformatics tool, though it could mention rate limits or error handling.

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 two sentences and mostly efficient, but the first sentence uses jargon ('Synthesis: one-call equivalent of the find_homologs prompt') that may be unclear. Still, it is concise and avoids unnecessary repetition.

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 presence of an output schema, the description does not need to detail return values, but it mentions returns (ranked hits with UniProt records). It could benefit from specifying that top_n controls the number of hits. Overall, it covers the main workflow.

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 low (33%: only sequence has a description). The description adds no parameter-specific details, even though it could elaborate on program options or top_n behavior. Most parameter semantics rely on the schema, which is sparse.

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 synthesis of the find_homologs prompt, running BLAST then resolving accessions to UniProt records. This verb+resource combination is specific and distinguishes it from siblings like blast_sequence (BLAST only) and gramene_homologs (different resolution method).

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 lacks explicit guidance on when to choose this tool over alternatives such as blast_sequence or gramene_homologs. It implies use for homology search with UniProt enrichment, but no when-not-to-use or prerequisite conditions are mentioned.

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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