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Jean — Molecular Biology & Genomics

primer_check

Read-only

Where a primer anneals on the open plasmid: 3'-anchored sites with identity % and the ✓/⚠/~/✗ verdict, graded at a bar you can move and that the answer states.

Input Schema

NameRequiredDescriptionDefault
_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.
primerYesprimer sequence 5'→3'.
_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.
thresholdsNothe identity boundaries the ✓/⚠/~/✗ verdict is cut at. Left unset, the run uses the bar your Primer Library is set to, and with no panel state the upstream SpliceCraft default — either way the bar it used comes back in `thresholds`, because a verdict whose cutoff is not stated cannot be checked. Move it to say what you are asking: screening a pool tolerates a lower `strong` than checking a clone does. Advanced.

Output Schema

NameRequiredDescriptionDefault
sitesYesannealing sites with identity %, mismatches, strand, the 3'-anchored footprint, and each one's tier and what that tier MEANS — read the tier rather than re-deriving it from the percentage, because the bar is a parameter
bestTierYesthe best site's tier: exact · strong · weak · marginal · none, or unknown when nothing was graded
siteCountYeshow many sites the seed found at all. Branch on this rather than on the length of `sites`: 0 is a real result and means the oligo's 3' end matches nowhere, not that it binds weakly
thresholdsYesthe four boundaries every verdict above was made against, and whether they came from your panel or from the upstream default — the same shape the `thresholds` parameter takes, so a run can be repeated at the bar it was graded at
bindingCountYeshow many sites are at or above the `strong` boundary — the ones expected to bind. More than one is a different experiment from one: a primer with two real sites gives two products, so a single clean band is not what this predicts
bestIdentityPctYesidentity of the best site, or 0 when nothing was found — a measurement, never a verdict

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed1 schema field changed
    • addedOutput schema / properties / bestIdentityPct / x-unit
      Added value: +"%"
  2. First observed

TDQS

A3.7/5.0
Behavior4/5

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

Annotations already declare readOnlyHint=true, destructiveHint=false and openWorldHint=false, so safety is covered. The description adds genuine behavior beyond that: sites are 3'-anchored, grading uses a four-level verdict cut at movable thresholds, and the bar actually used is echoed back in the response so the verdict is checkable. The default-source chain (Primer Library panel, then SpliceCraft default) is also disclosed.

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?

A single front-loaded sentence with no filler, and the core purpose comes first. The trailing clause ('graded at a bar you can move and that the answer states') is slightly convoluted and takes a second read, but nothing is redundant.

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?

Output schema exists, so return values need not be described, and the read-only annotations remove the safety burden. What remains — what 3'-anchored means in bases, whether both strands or circularity are handled — is left to the schema and output schema, a minor gap for a tool with nested objects and four parameters.

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 per-threshold semantics and the rationale for exact=99.999, so the schema already carries the parameter burden. The description only adds that the bar is movable and is reported back in the answer — useful framing but not new per-parameter meaning, so the baseline 3 holds.

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?

States a specific verb-and-resource: locate where a primer anneals on the open plasmid, returning 3'-anchored sites with identity % and a ✓/⚠/~/✗ verdict. The 'open plasmid' scoping implicitly distinguishes it from genome-wide siblings like check_primer_specificity or survey_off_targets, but no sibling is named explicitly.

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 rather than stated: the plasmid-scoped phrasing suggests when this applies, and the threshold note ('screening a pool tolerates a lower strong than checking a clone does') gives a real use-case cue. However, there is no explicit when-not or pointer to the alternative off-target/specificity tools an agent would otherwise confuse this with.

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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