jean — Molecular Biology & Genomics

recombine

Recombination between molecules — Gateway BP/LR (att sites), Cre/loxP, a serine integrase whose two half-sites you supply, plain homologous recombination through shared arms, or a CRISPR knock-in that keeps only products whose repair region contains every guide's cut. Emits the first product as a NEW record for downstream nodes.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`site1`	No	the recombinase's first half-site (e.g. attP). Case is meaningful: the lower-case middle is the overlap the enzyme crosses over in. Only applies when system is recombinase.
`site2`	No	the recombinase's second half-site (e.g. attB), same convention. Only applies when system is recombinase.
`_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.
`greedy`	No	permissive att core matching. Only applies when system is gateway-BP or gateway-LR. Advanced.
`guides`	No	protospacers whose cut must fall inside the repaired region — a product cut elsewhere by any of them is discarded and counted. Only applies when system is crispr-knock-in.
`system`	No	recombination system. Values: gateway-BP (Gateway BP (attB × attP → entry)), gateway-LR (Gateway LR (attL × attR → expression)), cre-lox (Cre / loxP), recombinase (Serine integrase (your two half-sites)), homologous (Homologous recombination (shared arms)), crispr-knock-in (CRISPR knock-in (guide-gated HR)).	gateway-LR
`_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.
`fragments`	No	the molecules to react — wire upstream `record` outputs here, or name library documents.
`homology_bp`	No	shortest homology arm that counts as a shared end. In bp. Only applies when system is homologous or crispr-knock-in.
`circular_only`	No	report only circular products.
`include_subject`	No	also include the node's subject as a reactant.
`multi_site_only`	No	keep only products where BOTH sites recombined (drops single-site intermediates). Only applies when system is gateway-BP or gateway-LR.

Output Schema

TableJSON Schema

Name	Required	Description
`sites`	Yes	per-input report of the recombination sites found
`record`	Yes	the first product, as a record
`products`	Yes	every product
`discarded`	Yes	CRISPR knock-in only: products dropped because a guide also cuts OUTSIDE the repair. A non-zero count is a finding about the guide, not a warning to swallow
`productCount`	Yes	number of products

Schema Changelog

Changes observed during successful MCP inspections.

First observedOct 20, 2026

TDQS

A3.9/5.0

Behavior4/5

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

Annotations declare readOnly=false, destructive=false, openWorld=false, so the safety profile is already partly covered, and the description is consistent with it. The description adds genuinely useful behavior the annotations do not: the output is emitted as a NEW record for downstream wiring, and for CRISPR knock-in only products whose repair region contains every guide's cut survive (others discarded and counted).

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Two sentences, front-loaded with the recombination scope and ending with the most decision-relevant output fact (new record for downstream nodes). The first sentence is long and runs through six systems, but each clause carries distinct information rather than filler.

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?

An output schema exists, so return values need no explanation, and the description adequately frames the six modes plus the product-emission behavior for a 12-parameter, zero-required tool. It does not tie the optional modifiers (include_subject, circular_only, multi_site_only) to outcomes, but the schema covers those individually.

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 schema already explains site1/site2, greedy, guides, homology_bp, circular_only, multi_site_only, include_subject and the _subject/_files shapes. The description adds only the CRISPR guide-gating rule, which is not parameter syntax; the 3 baseline for full schema coverage 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?

States a specific verb+resource (recombination between molecules) and enumerates the exact six systems it supports, which maps directly to the enum and separates it from neighboring assembly tools like gibson_assemble, ligate_fragments, or fusion_pcr. An agent can tell what this does without opening the schema.

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?

Usage is implied by the listed systems (Gateway BP/LR, Cre/loxP, integrase, homologous, CRISPR knock-in), so an agent can infer which mode applies to its scenario. However, it never states when to prefer this over overlapping siblings such as gibson_assemble or restriction_ligate, and offers no exclusions or prerequisites.

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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