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Jean — Molecular Biology & Genomics

design_bisulfite_primers

Design BSP or MSP primers for a methylation assay, on the CONVERTED strands: after bisulfite treatment every unmethylated C reads as T, which is a different template from the one every other designer sees.

Input Schema

NameRequiredDescriptionDefault
assayNoBSP = bisulfite sequencing PCR: primers avoid CpG sites so both methylated and unmethylated template amplify equally, and the methylation is read from the SEQUENCE afterwards. MSP = methylation-specific PCR: primers cover CpG sites so amplification ITSELF is the readout. They answer different questions and are not interchangeable. Values: BSP (BSP - amplify regardless of methylation), MSP (MSP - amplify only one state).BSP
_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.
max_gcNohighest acceptable GC. In %. Advanced.
max_tmNoprimers above this Tm are rejected outright. In °C. Advanced.
min_gcNolowest acceptable GC. The floor is low on purpose: after conversion every unmethylated C is a T, so converted DNA is genuinely GC-poor and an ordinary 40% floor rejects correct primers. In %. Advanced.
min_tmNoprimers below this Tm are rejected outright. In °C. Advanced.
opt_tmNotarget Tm; candidates rank by distance from it. Bisulfite-converted DNA is C-poor, so these run lower than an ordinary design. In °C.
min_cpgNoMSP ONLY. The fewest CpG sites a primer must cover, so it can discriminate methylated from unmethylated at all. In sites.
_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.
criteriaNowhich published criteria call a CpG island: Gardiner-Garden & Frommer 1987 as EMBOSS cpgplot encodes it, or the stricter Takai & Jones 2002, which excludes most Alu repeats. Values: cpgplot (Gardiner-Garden & Frommer (cpgplot)), takaiJones (Takai & Jones 2002 (promoter islands)).cpgplot
max_lengthNolongest primer considered. In nt. Advanced.
min_lengthNoshortest primer considered. In nt. Advanced.
opt_lengthNoprimer length the ranking prefers. In nt.
region_endNo0-based inclusive end. Unset = the whole sequence. Advanced.
max_resultsNohow many primer pairs to return, best first.
product_maxNolongest acceptable amplicon. In bp.
product_minNoshortest acceptable amplicon. In bp.
region_startNo0-based inclusive start of the region to design in. Unset = the whole sequence; pass the selection's start to scope to it. Advanced.
island_windowNosliding window over which C, G and CpG are counted (cpgplot -window); unset takes the preset's. In bp. Advanced.
min_non_cpg_cNoBSP ONLY. The fewest non-CpG cytosines the ORIGINAL sequence under a primer must carry - the rule that makes a BSP primer bisulfite-SPECIFIC, because those cytosines become T only if conversion worked. A primer with none anneals to untreated DNA just as well and the assay silently reports on template that was never converted. In nt.
design_in_islandNodesign inside this island only, by its rank in the reported list (1 = first). Unset designs anywhere in the region; the panel instead asks for an island to be picked.
island_min_lengthNominimum island length (cpgplot -minlen); unset takes the preset's. In bp. Advanced.
island_min_obs_expNominimum observed/expected CpG (cpgplot -minoe); unset takes the preset's. Advanced.
island_min_percentNominimum %C+%G (cpgplot -minpc); unset takes the preset's. In %. Advanced.
max_cpg_distance_from_3NoMSP ONLY. How close to the 3' end the last CpG must sit. A mismatch discriminates most strongly at the 3' end, because that is where the polymerase extends. In nt. Advanced.

Output Schema

NameRequiredDescriptionDefault
assayYeswhich assay was designed, echoed so a result never has to be guessed at
countYeshow many pairs were found
pairsYesthe primer pairs, best first: each with both oligos, their coordinates on the ORIGINAL unconverted sequence, Tm, GC, CpG count and the non-CpG C conversion check
forwardYesthe best pair's forward primer (wire into pcr_amplify)
islandsYesCpG islands in the record (EMBOSS cpgplot criteria) - what a methylation assay should be aimed at
reverseYesthe best pair's reverse primer
islandCountYeshow many CpG islands were found
methylatedPairsYesMSP: the pairs specific for the METHYLATED allele. Empty under BSP
unmethylatedPairsYesMSP: the pairs specific for the UNMETHYLATED allele - the other half of the assay, and the control that tells a negative from a failed reaction. Empty under BSP

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

B3.4/5.0
Behavior3/5

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

Annotations only declare the safety profile (readOnlyHint=false, destructiveHint=false, openWorldHint=false); the description's real contribution is the domain fact that the design template is bisulfite-converted DNA, which is genuinely non-obvious. It says nothing about what input record is expected (converted vs genomic), that a design is computed rather than a curated lookup, or what the returned panel contains beyond the existence of an output schema.

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 front-loaded sentence with the operative verb and mode first, then the justification. The trailing clause is explanatory rather than redundant, though 'a different template from the one every other designer sees' is slightly rhetorical for the information it carries.

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?

For a 25-parameter, nested-object tool that also performs CpG island detection (criteria, island_* params), the description is thin: it does not explain that islands are found first and can be targeted by rank, nor how BSP (CpG-avoiding) and MSP (CpG-covering) designs diverge, both of which are buried in the schema. It is minimally sufficient because the schema and output schema are rich, but it leaves real gaps.

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% and the enum for assay is documented in unusual depth, so the schema does the parameter work. The description adds no parameter-level meaning (no mention of min_non_cpg_c, min_cpg, design_in_island, or the island criteria) beyond restating the assay choice conceptually.

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 and resource ('Design BSP or MSP primers for a methylation assay') and pins the template to CONVERTED strands, which separates it conceptually from the generic designers in the sibling list. It never names an alternative tool (design_primers, design_primer_pairs, design_sequencing_primers) outright, so the differentiation stays implicit rather than operational.

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?

It implies the use case (methylation assays needing BSP or MSP primers) but gives no when-not guidance, no prerequisites about starting from an unconverted genomic record, and no pointer to follow-up tools such as check_methylation_block, check_primer_specificity or primer_check. An agent knows roughly what it is for but must infer the workflow position.

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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