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CovaSyn Chemistry Tools

covabio_sirna

Design siRNA candidates against a target mRNA sequence using Reynolds 2004 rules. Scores 19-mer windows for efficacy, GC content, thermodynamic asymmetry, and off-target risk. Returns ranked candidate list.

Parameters:
  target_sequence: Target mRNA sequence (DNA, minimum 21 nt).

Returns: {n_candidates, candidates: [{position, sense, antisense, score, gc_content}]}

Input Schema

NameRequiredDescriptionDefault
api_keyNo
target_sequenceYes

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A3.7/5.0
Behavior3/5

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

With no annotations, the description carries the full burden. It does disclose meaningful behavior: the scoring dimensions (efficacy, GC, thermodynamic asymmetry, off-target risk) and the 19-mer windowing approach. However, it never states this is a pure computation with no side effects, nor that an api_key credential is required, leaving safety/operational context thin.

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?

Front-loads the purpose in the first sentence and organizes parameters and returns compactly with no filler. The explicit Returns block is somewhat redundant since an output schema already exists, costing a small amount of space.

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 two-parameter tool, the description covers what it does, how it scores, the key input constraint, and the return shape. The only meaningful gap is the undocumented api_key parameter and absence of any usage routing context.

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 description coverage is 0%, so the description must compensate. It explains target_sequence well, adding the key constraint of minimum 21 nt and clarifying it is DNA even though the input is mRNA-derived. It says nothing about the api_key parameter, leaving one of two params undocumented.

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?

States a specific verb (Design) and resource (siRNA candidates against a target mRNA), and names the exact methodology (Reynolds 2004 rules) plus the scored criteria. An agent can distinguish this from sibling design/analysis tools like covabasic_reynolds or covabio_mrna without opening the schema.

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?

Usage is only implied: an agent infers this is the tool for designing siRNA from an mRNA sequence. There is no explicit when-to-use/when-not guidance, no mention of prerequisites, and no routing to alternatives among the many covabio/covabasic siblings.

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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