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Translate sequence

computase_translate_sequence
Read-onlyIdempotent

Translate DNA/RNA codons into proteins with a selected NCBI genetic code. Choose stop-codon handling: truncate at first stop or translate through, for raw or FASTA sequences.

Instructions

Translate complete codons with a selected NCBI genetic code.

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.
table_idNoNCBI genetic-code table identifier.
stop_handlingNoStop-codon handling policy.translate-through

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
proteinYesTranslated protein, with stops represented as '*'.
table_idYesNCBI genetic-code table identifier.
parametersNoEffective operation parameters, excluding the input sequence.
table_nameYesPrimary NCBI genetic-code table name.
codon_countYesNumber of complete input codons.
stop_handlingYesEffective stop-codon handling policy.
stopped_earlyYesWhether translation was truncated at an encountered stop codon.
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?

Annotations already declare the tool read-only, idempotent, and non-destructive. The description adds some behavioral context by restricting translation to complete codons and allowing a selectable genetic-code table, but it leaves undefined edge behaviors like partial trailing codons or stop-codon outcomes, which are only implied by the schema.

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 concise sentence with no filler. It front-loads the action ('Translate complete codons') and includes the key qualifier ('selected NCBI genetic code'), making it appropriately sized for a straightforward operation.

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 rich input schema, output schema, and annotations carry most of the operational details, making the description adequate for invoking the tool. However, it is slightly incomplete because it does not position the tool against the related ORF-enumeration sibling or clarify partial-codon handling.

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 sequence, table_id, and stop_handling are already fully documented. The description adds little beyond restating the genetic-code selection, so the schema-based baseline 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 names a specific verb ('Translate') and resource ('complete codons'), with a meaningful qualifier ('selected NCBI genetic code'). This clearly distinguishes the tool from siblings such as reverse_complement or scan_motif, and 'complete codons' helps separate it from ORF enumeration.

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 the intended use—translating a nucleotide sequence with a chosen genetic code—but it does not explicitly say when to choose this tool over computase_enumerate_orfs or any other sibling. There is no when-not-to-use guidance or mention of alternatives.

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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