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Scan motif

computase_scan_motif
Read-onlyIdempotent

Scan nucleotide sequences for IUPAC motifs on forward, reverse, or both strands, with configurable overlapping matches and result limits.

Instructions

Scan an IUPAC motif on the forward, reverse, or both strands.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
motifYesIUPAC nucleotide pattern.
strandNoStrand orientation to scan.forward
sequenceYesRaw nucleotide sequence or one FASTA record; IUPAC codes are accepted. The normalized sequence is limited to 5,000,000 nucleotides.
max_matchesNoMaximum returned sites.
overlappingNoReport overlapping sites.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
motifYesNormalized IUPAC motif.
strandYesRequested strand policy.
matchesYesMotif occurrences in coordinate order.
truncatedYesWhether occurrences were omitted by max_matches.
parametersNoEffective operation parameters, excluding the input sequence.
total_foundYesTotal occurrences before result limiting.
computase_versionNoComputase version used for the computation.0.1.1
coordinate_systemNo0-based-half-open
Behavior3/5

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

Annotations already establish readOnly, idempotent, and non-destructive behavior, so the bar is lower. The description adds minimal behavioral context beyond stating the scanner action; it does not disclose return patterns, edge cases, or other behaviors, but it does not contradict the annotations.

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 a single sentence, front-loaded with the action, and contains no unnecessary words. It is highly concise and easy to parse, earning a top score for conciseness.

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?

The description is brief, but the detailed schema and output schema compensate for missing return-value details. Given the moderate complexity and strong structured metadata, the description is complete enough, though it could hint at additional behaviors like overlapping or match limits.

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 100%, so the baseline applies. The description mentions 'IUPAC motif' and 'strands' but does not add any parameter-specific semantics beyond what the schema already provides. The schema adequately documents all five parameters.

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 uses a specific verb 'Scan' and clearly identifies the resource ('IUPAC motif') and the strands it operates on, which distinguishes it from sibling tools like ORF enumeration or reverse complement. It is unambiguous about the tool's core function.

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 provides no explicit guidance on when to use this tool compared to alternatives, nor any prerequisites or exclusions. Usage is only implied through the description itself, with no mention of sibling tools or specific use cases.

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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