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Summarize sequence

computase_summarize_sequence
Read-onlyIdempotent

Compute nucleotide composition, GC uncertainty, and GC skew from a raw sequence or FASTA record.

Instructions

Summarize composition, GC uncertainty, and GC skew.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
sequenceYesRaw nucleotide sequence or one FASTA record; IUPAC codes are accepted. The normalized sequence is limited to 5,000,000 nucleotides.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
lengthYesNormalized sequence length.
gc_skewYesConcrete-base (G-C)/(G+C), or null when no concrete G/C exists.
gc_percentYesGC percentage over residues with determinate GC status.
parametersNoEffective operation parameters, excluding the input sequence.
compositionYesCounts for every residue present.
dinucleotidesYesCounts of overlapping adjacent residue pairs.
sequence_typeYesDetected nucleotide alphabet.
gc_max_percentYesMaximum possible GC percentage under IUPAC resolutions.
gc_min_percentYesMinimum possible GC percentage under IUPAC resolutions.
ambiguous_countYesNumber of non-ACGT or non-ACGU IUPAC residues.
computase_versionNoComputase version used for the computation.0.1.2
Behavior3/5

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

The annotations already declare readOnlyHint=true, idempotentHint=true, and destructiveHint=false, so the safety profile is clear. The description adds the output metrics (composition, GC uncertainty, GC skew) but does not describe behavior such as normalization or how input limits are handled beyond what the schema already states. No contradiction with 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, front-loaded sentence with no filler or redundant restating of the title. Every word adds value by naming the specific analysis outputs.

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 single parameter, rich annotations, and the presence of an output schema, the description is largely complete. It names the key computed metrics, and the output schema covers return details. It falls slightly short only by not addressing usage context relative to siblings, but this is a minor gap.

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%, and the one required parameter 'sequence' has a descriptive schema entry including accepted inputs and length limits. The tool description adds no additional meaning beyond what the schema already provides, so the baseline score of 3 is appropriate.

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 ('Summarize') with a clear resource and names three concrete outputs: composition, GC uncertainty, and GC skew. This distinguishes it from siblings like reverse_complement or translate_sequence, which perform transformations rather than summary statistics.

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?

There is no explicit guidance on when to use this tool versus the sibling tools. The purpose implies it is for sequence summary statistics rather than transformations or motif scanning, but no when-to-use or when-not-to-use conditions are stated, leaving the agent to infer selection criteria.

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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