motif_finderFind (overlapping) occurrences of an IUPAC motif on either strand, allowing mismatches.
| Name | Required | Description | Default |
|---|---|---|---|
| motif | Yes | Query motif; IUPAC ambiguity codes (R Y S W K M B D H V N) allowed. | |
| sequence | Yes | Nucleotide sequence (raw or FASTA; IUPAC accepted). | |
| maxMismatches | No | Maximum allowed mismatches per match. | |
| searchReverseStrand | No | Also search the reverse strand. |
Changes observed during successful MCP inspections. Dates show when Glama detected each change.
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
The description adds behavioral context beyond annotations by specifying overlapping matches, allowance of mismatches, and dual-strand search. Annotations already indicate read-only and idempotent behavior, so the description effectively supplements these with operation details.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
A single 13-word sentence that front-loads the action and includes key qualifiers. Every word contributes meaning, with no redundancy or filler. Ideal conciseness for quick parsing.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
The description lacks output format details (e.g., positions, list of matches) and does not address limits (e.g., sequence length). With no output schema, the description should compensate, but it does not, leaving an AI agent with incomplete invocation context.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Input schema has 100% description coverage, so the schema already documents all four parameters. The description adds no new semantic information beyond rephrasing the tool's purpose. Baseline score of 3 is appropriate since schema carries the burden.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states the verb 'Find' and the resource 'occurrences of an IUPAC motif', with specific qualifiers like overlapping, either strand, and allowing mismatches. This makes the tool's exact functionality unambiguous and distinguishes it from sibling tools like 'find_orfs' or 'restriction_sites'.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description implicitly defines when to use this tool (motif finding in nucleotide sequences) but lacks explicit guidance on when not to use it or which sibling tools are alternatives. An agent could reasonably infer usage, but clearer direction would improve selection confidence.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.