Skip to main content
Glama
musharna

plant-genomics-mcp

consensus_homologs

Identifies plant gene homologs by combining UniProt, Gramene, and NCBI BLAST results, deduplicating hits, and ranking by source count and identity.

Instructions

Synthesis: cross-source homology consensus. Resolves UniProt + FASTA sequence, then runs Gramene homology calls and NCBI BLAST in parallel. Dedupes hits by normalized locus token and scores by n_sources * mean_identity — Gramene contributes identity=1.0, BLAST contributes pident/100.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
locusYes
organismNoPlant organism — accepts canonical slug (arabidopsis_thaliana), scientific or common name, or NCBI taxidarabidopsis_thaliana
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, the description fully discloses the multi-step process: sequence resolution, parallel homology calls, deduplication, and scoring formula. It is transparent about the algorithm's behavior.

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?

Description is concise and well-structured as a single paragraph, efficiently covering the synthesis approach without redundancy.

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?

For a tool with 3 parameters and an output schema, the description sufficiently explains the synthesis logic. It could mention output format, but output schema covers that.

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 only 33%. The description does not add meaning to 'locus' or 'top_n' beyond the schema. It explains the tool's process but not how parameters influence results.

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?

Description clearly states it produces a cross-source homology consensus by resolving sequences and running Gramene and NCBI BLAST in parallel, then deduping and scoring. This is distinct from sibling tools like gramene_homologs or blast_sequence.

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?

No explicit guidance on when to use this tool versus alternatives. The description implies it's for comprehensive homology searches, but does not state conditions or exclusions.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

Install Server

Other Tools

Latest Blog Posts

MCP directory API

We provide all the information about MCP servers via our MCP API.

curl -X GET 'https://glama.ai/api/mcp/v1/servers/musharna/plant-genomics-mcp'

If you have feedback or need assistance with the MCP directory API, please join our Discord server