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Jean — Molecular Biology & Genomics

screen_guides

Read-only

Screen guide spacers the way CHOPCHOP does before it accepts them: GC gate, self-complementary hairpins inside the spacer, and hairpins against the sgRNA backbone.

Input Schema

NameRequiredDescriptionDefault
ggNothe construct starts the transcript GG — upstream's `-gg` REPLACES the spacer's first two bases with G (T7 preference), it does not lengthen it. Advanced.
pre_gNothe construct prepends a single 5' G (upstream's `-preG`) — this one lengthens the scanned string, and upstream's fixed 17-window loop then never reaches its last bases. Advanced.
_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.
spacersYesthe protospacers to screen (20 nt for SpCas9) — wire `topSpacer` or the spacers out of a design run, or list them.
_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.
backboneNowhich sgRNA backbone the spacer will be cloned into — the hairpin test is against this. Values: original (original gRNA backbone), extended (extended backbone (Cas9-GFP tracking)).original

Output Schema

NameRequiredDescriptionDefault
cleanYesthe spacers that passed the GC gate and flagged no hairpin — the ones to take forward
countsYesupstream's own four summary counts: total, after the GC screen, with a self hairpin, with a backbone hairpin
screenedYesper spacer: GC, whether it was dropped by the GC gate, the two hairpin verdicts, and every flagged 4-mer with its position
backboneLabelYeswhich backbone the run screened against

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A3.8/5.0
Behavior4/5

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

Annotations already declare readOnlyHint=true and destructiveHint=false, so safety is covered; the description adds genuine behavioral content by disclosing the exact screening criteria (GC gate, intra-spacer hairpins, backbone hairpins) and that the behavior mirrors CHOPCHOP. It stops short of stating pass/fail thresholds or how rejected spacers are reported, but the output schema covers the return shape.

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 with the core action front-loaded and the three checks listed in order of operation. No filler, no restatement of the tool name.

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?

With annotations, a full output schema, and complete parameter descriptions, the description only needs to convey purpose and algorithm, which it does. The only notable omission is the GC threshold or rejection criteria, but that is arguably output-schema territory.

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%, including detailed notes on gg, pre_g, backbone, and spacers, so the schema carries the parameter burden. The description adds no parameter-specific meaning beyond what the schema already states; baseline 3 applies.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description names a specific verb (screen) and resource (guide spacers) and enumerates the three checks performed — GC gate, self-complementary hairpins within the spacer, and hairpins against the sgRNA backbone. That is enough to distinguish it from siblings like fold_guide or search_off_targets, though it never explicitly names an alternative.

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 phrase 'before it accepts them' implies this is a pre-acceptance QC step, but there is no explicit when-to-use guidance, no exclusions, and no pointer to an alternative tool for off-target or efficacy scoring. Usage must be inferred.

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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