Jean by Melad Labs

design_ish_probes

Read-only

Design an in-situ hybridization probe against the subject: tile it into candidate oligos that meet a melting-temperature, G+C and composition specification, screen them for off-target binding against an alignment and for k-mers abundant in a reference, and gather the survivors into the set that images best.

Input Schema

Name	Required	Description	Default
`dnac1`	No	concentration of the higher-concentration strand, typically the probe, in the melting-temperature calculation (OligoMiner `--dnac1`). In nM.
`dnac2`	No	concentration of the lower-concentration strand, typically the target (OligoMiner `--dnac2`). The Tm uses dnac1 − dnac2/2, so equal values halve the effective concentration. In nM.
`_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.
`max_gc`	No	highest percent G+C to accept. In %.
`max_tm`	No	highest melting temperature to accept. In °C.
`min_gc`	No	lowest percent G+C to accept. In %.
`min_tm`	No	lowest melting temperature to accept, AFTER the formamide correction. In °C.
`origin`	No	coordinate of the subject's first base, when it is a window cut from a larger sequence. Read from a UCSC-style `range=` header when the subject carries one. Advanced.
`probes`	No	how many probe sets to return. Only applies when oligos_per_probe is set.
`sodium`	No	monovalent cation concentration of the hybridization buffer. In mM.
`overlap`	No	report every window that qualifies, including overlapping ones. Off by default because overlapping oligos cannot be used together in one probe. Advanced.
`rank_by`	No	feature that ranks the sets inside that band. Values: centrality (Centrality on the region), size (Compactness), homogeneity (Even spacing). Only applies when oligos_per_probe is set. Advanced.	size
`spacing`	No	bases forced between consecutive oligos. In nt. Advanced.
`_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.
`filter_by`	No	feature that defines the band of acceptable sets. Values: centrality (Centrality on the region), size (Compactness), homogeneity (Even spacing). Only applies when oligos_per_probe is set. Advanced.	centrality
`formamide`	No	formamide in the hybridization buffer; it lowers every melting temperature by about 0.65 °C per percent. In %.
`kmer_dump`	No	`jellyfish dump` of a genome's k-mer dictionary, for a reference too large to count here: `jellyfish count -m 18 -L 5` then `jellyfish dump -c -L 5` keeps only the k-mers a screen at 5 acts on. Advanced.
`max_length`	No	longest oligo to accept; the tiler grows a window until one fits, so a wide range yields more probes. In nt.
`min_length`	No	shortest oligo to accept. In nt.
`prohibited`	No	comma-separated subsequences an oligo may not contain; the default bans homopolymer runs, which hybridize promiscuously. Advanced.	AAAAA,TTTTT,CCCCC,GGGGG
`kmer_length`	No	k, the k-mer length counted in kmer_reference (OligoMiner's README builds 18); a dump carries its own. In nt. Only applies when kmer_reference is set.
`screen_mode`	No	trained model (recovers usable probes near repeats) · unique alignment only (strict) · no alignment at all (for a sequence that should be absent). Values: lda (Trained model), unique (Unique alignment only), zero (No alignment at all). Only applies when alignment_sam is set.	lda
`alignment_sam`	No	SAM the candidates were aligned with, for off-target screening. Without it the oligos are returned UNSCREENED and the result says so.
`kmer_canonical`	No	count a k-mer and its reverse complement as one (jellyfish -C). Off as OligoMiner's dictionary is; for a dump it must match how the dictionary was counted. Advanced.
`kmer_reference`	No	FASTA of the reference to count k-mers in, for OligoMiner's k-mer screen. Counted here, so a whole genome belongs in kmer_dump instead. Without either the oligos are returned with k-mer abundance UNCHECKED and the result says so.
`kmer_threshold`	No	drop an oligo holding any k-mer that occurs this many times or more in the reference.
`filter_threshold`	No	width of the band around the best set, as a fraction of its own value. Only applies when oligos_per_probe is set. Advanced.
`oligos_per_probe`	No	oligos to gather into one probe. Leave unset to return every surviving oligo instead of a set.
`hybridization_temperature`	No	temperature the specificity model was trained at. Only these six exist; the coefficients change sign across the range, so an intermediate value is a different model rather than a blend. In °C. Only applies when alignment_sam is set.
`max_off_target_probability`	No	keep an oligo whose modelled chance of a real off-target site is below this. Only applies when alignment_sam is set. Advanced.

Output Schema

Name	Required	Description
`kmer`	Yes	the k-mer screen's reading of each oligo it saw: its start, the highest count charged to it, and whether it was kept. Absent when no k-mer reference or dump was given
`oligos`	Yes	every oligo that survived all stages, in target order
`probes`	Yes	the chosen probe sets, best first, each with its oligos and its three scores
`stages`	Yes	what each stage took in, put out, and removed - with the reasons named
`coverage`	Yes	the coverage track, gaps, spacings and the Tm/G+C distributions a renderer draws
`oligoCount`	Yes	how many oligos survived
`explanation`	Yes	the derivation chain: conclusion, interpretation and machinery, generated from this run
`coveredFraction`	Yes	fraction of the target covered by at least one surviving oligo (0-1)

Schema Changelog

Changes observed during successful MCP inspections.

Changed7 schema fields changedOct 21, 2026

addedInput schema / properties / kmer_canonical

Added value: +{
+  "default": false,
+  "description": "count a k-mer and its reverse complement as one (jellyfish -C). Off as OligoMiner's dictionary is; for a dump it must match how the dictionary was counted. Advanced.",
+  "type": "boolean"
+}

addedInput schema / properties / kmer_dump

Added value: +{
+  "description": "`jellyfish dump` of a genome's k-mer dictionary, for a reference too large to count here: `jellyfish count -m 18 -L 5` then `jellyfish dump -c -L 5` keeps only the k-mers a screen at 5 acts on. Advanced.",
+  "type": "string"
+}

addedInput schema / properties / kmer_length

Added value: +{
+  "default": 18,
+  "description": "k, the k-mer length counted in kmer_reference (OligoMiner's README builds 18); a dump carries its own. In nt. Only applies when kmer_reference is set.",
+  "maximum": 31,
+  "minimum": 8,
+  "type": "number"
+}

addedInput schema / properties / kmer_reference

Added value: +{
+  "description": "FASTA of the reference to count k-mers in, for OligoMiner's k-mer screen. Counted here, so a whole genome belongs in kmer_dump instead. Without either the oligos are returned with k-mer abundance UNCHECKED and the result says so.",
+  "type": "string"
+}

addedInput schema / properties / kmer_threshold

Added value: +{
+  "default": 5,
+  "description": "drop an oligo holding any k-mer that occurs this many times or more in the reference.",
+  "maximum": 100000,
+  "minimum": 1,
+  "type": "number"
+}

addedOutput schema / properties / kmer

Added value: +{
+  "description": "the k-mer screen's reading of each oligo it saw: its start, the highest count charged to it, and whether it was kept. Absent when no k-mer reference or dump was given"
+}

changedOutput schema / required

Previous value: -[
-  "probes",
-  "oligos",
-  "oligoCount",
-  "coveredFraction",
-  "stages",
-  "explanation",
-  "coverage"
-]New value: +[
+  "probes",
+  "oligos",
+  "oligoCount",
+  "coveredFraction",
+  "stages",
+  "kmer",
+  "explanation",
+  "coverage"
+]

First observedOct 20, 2026

TDQS

B3.4/5.0

Behavior3/5

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

Annotations already declare readOnlyHint=true, destructiveHint=false and openWorldHint=false, so the safety profile is covered. The description adds pipeline-level behavior (tiling, off-target screening, k-mer screening, set assembly), but omits the important behavioral fact that omitting alignment_sam or kmer_reference returns UNSCREENED/UNCHECKED oligos — that disclosure lives only in the schema. It also says nothing about runtime, result size, or the single-set versus all-oligos output mode.

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?

One sentence, front-loaded with the verb and resource, and every clause maps to a distinct pipeline stage rather than padding. It is dense but not redundant; a light structural break (e.g. separating the screening stages) would improve scanability.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

With an output schema present and full parameter documentation, the description only needs to frame the workflow, which it does. For a 30-parameter tool, though, it should flag the two operating modes (single gathered probe set when oligos_per_probe is set, versus every surviving oligo otherwise) and the unscreened fallback, since those change what an agent gets back.

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% across all 30 parameters, so the schema carries the semantics. The description only gestures at a few of them ('melting-temperature, G+C and composition specification', 'alignment', 'reference'), adding essentially no meaning beyond what the parameter descriptions already provide. Baseline 3 is appropriate.

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 ('Design an in-situ hybridization probe against the subject') and then enumerates the pipeline stages, so an agent knows exactly what the tool produces. It does not, however, distinguish itself from the closely related in-situ siblings (design_hcr_probes, design_merfish_probes, design_xenium_probes, design_padlock_probes), which is the main ambiguity an agent faces here.

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 only implied by the described workflow: an agent can infer that it needs a subject plus optional alignment/k-mer references to get screened probes. There is no explicit when-to-use statement, no when-not-to-use, and no naming of the sibling probe-design tools as alternatives.

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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