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CovaSyn Chemistry Tools

covabio_oligo

Compute oligonucleotide properties: melting temperature (Tm via SantaLucia 1998 nearest-neighbor), GC content, molecular weight, extinction coefficient, hairpin detection, and self-complementarity check.

Parameters:
  sequence: Nucleotide sequence (e.g. "ATCGATCG").
  oligo_type: "DNA" (default) or "RNA".

Returns: {tm_celsius, gc_content, molecular_weight, hairpin_detected, self_complementary}

Input Schema

NameRequiredDescriptionDefault
api_keyNo
sequenceYes
oligo_typeNoDNA

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A3.5/5.0
Behavior3/5

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

No annotations are provided, so the description carries the full behavioral-disclosure burden. It transparently describes the computation and return fields, including the Tm method, but omits operational details such as whether an API key is required, input length/validity constraints, and error behavior.

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 front-loaded and clearly sectioned into purpose, parameters, and returns. It contains no filler sentences, and the return list is short enough to be useful despite an output schema existing.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

The output schema exists, so return values need not be explained, but the description still omits the api_key parameter and any usage context. With no annotations and 0% schema description coverage, the definition is minimally adequate for a simple compute tool but leaves clear gaps.

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 documents sequence with an example and oligo_type with allowed values and default, but it completely omits the api_key parameter, leaving one of three parameters 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?

The description states a specific verb and resource: compute oligonucleotide properties. It enumerates the exact properties computed (Tm, GC content, molecular weight, extinction coefficient, hairpin detection, self-complementarity) and names the Tm algorithm, making it distinct from sibling tools focused on proteins, mRNA, siRNA, or general sequence utilities.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description explains what the tool does but gives no guidance on when to use it versus alternatives such as covabio_sequence_utils or other covabio_* tools. There are no exclusions, prerequisites, or routing cues.

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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