Skip to main content
Glama
musharna

plant-genomics-mcp

consensus_homologs

Resolve plant gene homologs by combining and scoring evidence from UniProt, Gramene, and NCBI BLAST to produce a consensus ranking.

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 explains the algorithmic steps: resolving sequences, parallel homology calls, deduplication, and scoring formula. It discloses that Gramene contributes identity=1.0 and BLAST contributes pident/100, offering good transparency.

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?

The description is three sentences, front-loaded with a one-sentence summary, and each sentence conveys essential information without redundancy. Highly concise.

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 tool's complexity (cross-source, parallel, scoring) and presence of an output schema (explaining return values), the description is largely complete. It covers the algorithm but lacks error handling or fallback behavior.

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%, and the description does not explain individual parameters beyond what is in the schema. It fails to compensate for low coverage, leaving ambiguity about the meaning of 'locus' and acceptable values for 'organism'.

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 starts with 'Synthesis: cross-source homology consensus' and details the pipeline involving UniProt, FASTA, Gramene, and BLAST. It clearly distinguishes from sibling tools like gramene_homologs and blast_sequence by combining multiple sources.

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 use for cross-source consensus but does not explicitly state when to use this tool versus alternatives like gramene_homologs or blast_sequence. It provides context but no 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