jean — Molecular Biology & Genomics

translate_sequence

Read-only

Translate the subject DNA to protein (Biopython Bio.Seq.translate semantics). The SUBJECT is the selection when there is one, the named feature when feature is given, and the whole record otherwise — the region output says which, so never paste bases in to scope it.

Input Schema

TableJSON Schema

Name	Required	Description
`cds`	No	strict CDS: require a length multiple of 3, a start codon and a terminal stop (errors otherwise). Advanced.
`table`	No	NCBI genetic-code table id (1 = standard).
`_files`	No	The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
`feature`	No	translate this annotated coding feature by NAME instead of the selection (e.g. "ADH1"). A name the record does not annotate is refused with the names it does.
`reverse`	No	read the region as the reverse complement. Stated explicitly this always wins; left out, the selection's or the feature's own strand decides. Advanced.
`to_stop`	No	stop at the first stop codon instead of emitting the stop symbol.
`_subject`	No	The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.

Output Schema

TableJSON Schema

Name	Required	Description
`length`	Yes	protein length in residues
`region`	Yes	what was translated, and on which strand
`protein`	Yes	the translated protein

Schema Changelog

Changes observed during successful MCP inspections.

First observedOct 20, 2026

TDQS

A4.3/5.0

Behavior4/5

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

Annotations already cover the safety profile (readOnly, non-destructive), and the description adds behavioral context: Biopython translation semantics, how the subject is determined, and that the region output indicates scope. It does not cover error handling or return format beyond that, but the output schema handles returns.

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?

Two sentences, front-loaded with the core purpose, then the critical scoping rule. No wasted words, and the warning is placed at the end for emphasis.

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?

Given the rich output schema, full parameter descriptions, and annotations, the description provides the missing usage warning and translation semantics. Nothing essential for correct invocation is absent.

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 coverage is 100% and all parameters are well-documented in the schema; the description adds only the high-level subject logic, which is already reflected in the schema's _subject description. Baseline 3 is appropriate when the schema does the heavy lifting.

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?

States a specific verb (Translate) and resource (subject DNA to protein), and specifies the direction, which distinguishes it from back_translate. The clarification of SUBJECT scoping (selection/feature/whole record) further differentiates it from tools requiring explicit sequence input.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Provides clear context for how to use it: define the SUBJECT via selection or feature, and explicitly warns 'never paste bases in to scope it.' No when-not or alternative tools are named, so no exclusions, but the context is sufficient.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

All jean — Molecular Biology & Genomics tools Inspect

Try in Browser

One endpoint for every MCP toolRayrun runs every MCP server behind one URL and holds the credentials. Each call is decided per client, tool, and argument, then recorded.ray.runAd

Glama MCP Gateway

Add one secure layer between your agents and this server.

Resources

Need Help?