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jean — Molecular Biology & Genomics

crispr_design_library

Read-only

Turn the open record's annotated targets into an ORDERABLE sgRNA oligo pool: the best N guides per target, filtered at order time (Pol-III terminator, Graf inactive motif, cloning-enzyme site, minimum on-target score), each composed into the oligo a synthesiser makes — the vector's cloning overhangs around the spacer plus, optionally, one of CRISPOR's eleven subpool barcodes. A spacer that serves two overlapping targets takes ONE well, and every candidate a filter held back is counted by reason, so a short pool says which rule shortened it. It designs a library; it does not analyse one. No recommended representation, MOI or read depth is embedded — the screen-scale arithmetic is in the editor panel, where the numbers are the user's.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
moiNomultiplicity of infection, 0 to leave it unplanned. Joung et al. 2017 recommends <0.3 so most cells take at most one perturbation; reported, never applied. Advanced.
rankNowhich on-target score orders the candidates. A guide the chosen model cannot score is left unranked, never dropped. Rule Set 3 is deliberately not offered here: its weights are a 9.8 MB download the editor fetches on demand, and this engine is headless and cannot fetch — offering it would return an unranked pool that looked ranked.ruleSet1
_filesNoThe 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.
_subjectNoThe 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.
nucleaseNothe nuclease (PAM + spacer length) to scan for. Values: SpCas9 (SpCas9: NGG (3')), SpCas9-NG (SpCas9-NG: NG (3')), SpG (SpG: NGN (3')), SpRY (SpRY: NRN (3')), xCas9 (xCas9: NG (3')), SaCas9 (SaCas9: NNGRRT (3')), SaCas9-KKH (SaCas9-KKH: NNNRRT (3')), AsCas12a (AsCas12a: TTTV (5')), LbCas12a (LbCas12a: TTTV (5')), enAsCas12a (enAsCas12a: TTTV (5')).SpCas9
barcode_idNoCRISPOR subpool barcode id, 0 for none — lets several sub-libraries share one synthesis array and amplify apart. Advanced.
target_typeNoannotation type to take as the targets, one pool entry per feature of that type (`CDS`, `gene`, …). Leave unset to treat the whole record as a single target — which is what a saturating-mutagenesis pool over one locus wants.
exclude_grafNodrop guides matching a Graf 2019 inactive motif (the TT/GCC classes).
custom_prefixNoyour vector's 5' cloning overhang. BOTH sides must be given, or the pool stays on pLentiGuide — that is upstream's rule, reproduced. Advanced.
custom_suffixNoyour vector's 3' cloning overhang. Advanced.
exclude_poly_tNodrop guides whose spacer carries a Pol-III (TTTT) terminator.
representationNocells you intend to keep carrying EACH guide. Joung et al. 2017 recommends >500; the default here is the neutral 1, not that recommendation, so the plan is the identity until you choose a scale. Advanced.
reads_per_oligoNosequencing reads per guide in the readout. Joung et al. 2017 recommends >500 for a screen (>100 to QC the cloned library); the default here is the neutral 1. Advanced.
guides_per_targetNohow many guides to take per target, best-ranked first.
restriction_enzymesNocloning enzymes whose recognition site must NOT appear in the spacer — a hit drops the guide from the pool. Advanced.
transduction_efficiencyNofraction of cells that take up a construct, 0-1 — sizes the transduction back up from the cells you need to keep. Advanced.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
countYesoligos in the pool
oligosYesone row per selected guide: target, spacer, coordinates, rank score, Graf class and the oligo to order
coverageYesthe screen's scale at the numbers given: cells to keep, cells to transduce, reads to buy, guides the depth expects to miss, and `belowGuidance` naming which of Joung et al. 2017's figures the plan falls short of
perTargetYesper target: candidates, selected, shortfall, and what each filter held back
oligoLengthYeslength of every oligo, for a synthesis quote (null when the pool is mixed)
distinctSpacersYesdistinct spacers — the number the screen's complexity is set by

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4.4/5.0
Behavior5/5

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

Annotations already declare this as a safe, read-only, non-destructive, non-open-world operation. The description adds rich behavioral context beyond annotations: order-time filtering, deduplication of overlapping targets into one well, per-reason counting of held-back candidates, the headless engine's inability to fetch Rule Set 3 weights, and the deliberate absence of recommended representation/MOI/read depth.

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?

The purpose is front-loaded in the first sentence, and the description is information-dense rather than repetitive. It is somewhat long and ornate, with clauses like 'every candidate a filter held back is counted by reason' that could be tightened, but each sentence contributes useful scope or behavioral detail.

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 complex 16-parameter nested schema, full parameter descriptions, annotations, and an output schema, the description provides enough context to call the tool correctly. It covers purpose, filtering behavior, synthesis-ready output, limitations, and what is intentionally not embedded, without needing to explain return values.

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 documents all 16 parameters in detail, including advanced flags and their defaults. The description adds some framing (best N guides per target, optional barcode, both custom overhangs required) but mostly reiterates what the schema provides, so the 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?

States a specific verb and resource: turning the open record's annotated targets into an ORDERABLE sgRNA oligo pool, with best-N guides per target and synthesis-ready oligo composition. It explicitly distinguishes itself from analysis tools ('It designs a library; it does not analyse one') and from generic guide design by emphasizing orderable pools, cloning overhangs, and subpool barcodes.

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?

Gives clear context for use: designing an orderable sgRNA pool from an open record's annotated targets, and states what it does not do ('does not analyse one'). It also notes that representation, MOI, and read depth are not embedded and points to the editor panel for screen-scale arithmetic. However, it does not explicitly name alternative sibling tools such as crispr_design_guides or when to choose them.

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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