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Summarize sequence

computase_summarize_sequence
Read-onlyIdempotent

Summarize DNA/RNA sequence composition, GC uncertainty, and GC skew to provide a quick overview of key sequence characteristics.

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.0.1.1
Behavior3/5

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

Annotations already declare readOnlyHint, idempotentHint, and destructiveHint=false, covering the safety profile. The description adds that it summarizes composition and GC-related metrics, which is useful context but does not detail additional behavior like output format or side effects, though the output schema likely covers that.

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?

A single sentence that directly states the tool's function without waste. Every word contributes meaning.

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

Completeness5/5

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

For a simple, single-parameter tool with complete schema coverage, annotations, and an output schema present, the description sufficiently conveys the tool's scope. It covers the key outputs and there are no obvious 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?

The schema fully documents the single 'sequence' parameter, including accepted formats (raw or FASTA), IUPAC codes, and length limit. The description adds no parameter information, so the schema carries the burden, meeting the baseline.

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 the specific verb 'summarize' with the resource 'sequence' and names specific outputs: composition, GC uncertainty, and GC skew. This clearly distinguishes it from siblings like scan, enumerate, reverse complement, and translate.

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 implies this is for obtaining a summary of sequence characteristics but does not explicitly state when to use it over alternatives. No exclusions or alternative tool references are given, but the distinct purpose is self-evident.

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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