jean — Molecular Biology & Genomics

design_sequencing_primers

Design a WALK of sequencing primers that reads a whole region, not one pair: tiled reads with confirmed overlap, on both strands by default, plus the coverage the walk actually achieves and any stretch it cannot reach. This is the 'how do I read all 6 kb of this construct' question, which a single pair does not answer. Read length and dead zone default to a named facility's published figures (MSU RTSF, ABI 3730XL) rather than to round numbers.

Input Schema

TableJSON Schema

Name	Required	Description
`_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.
`overlap`	No	confirmed overlap required between consecutive reads on one strand. Overlap is what turns abutting reads into a contig. Default 100 has NO published source and is a judgement, which is why it is stated rather than dressed as a figure. In bp.
`_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.
`dead_zone`	No	bases at the start of a read that are not trustworthy. Default 35 is the LONGEST the same source warns about (it says the first 25-35 bases are poor), so an untouched walk is the cautious reading in both directions. In bp. Advanced.
`target_tm`	No	target melting temperature for each primer in the walk. In °C. Advanced.
`min_length`	No	shortest acceptable primer. In bp. Advanced.
`region_end`	No	0-based inclusive end of the region to read. Unset = the whole template. Advanced.
`read_length`	No	usable bases per read, AFTER the dead zone. Default 800 is the shortest read MSU RTSF Genomics Core, Sanger Sequencing Best and Worst Practices (2024-04-25), ABI 3730XL promises (it quotes 800-900), which is the cautious end of a published range rather than a round number. In bp.
`both_strands`	No	read every base from both directions - what a sequencing facility means by double-stranded coverage, and the standard for anything deposited or published.
`region_start`	No	0-based inclusive start of the region to read. Unset = the whole template. Advanced.

Output Schema

TableJSON Schema

Name	Required	Description
`gaps`	Yes	stretches no read reaches - empty means the region is fully read
`used`	Yes	the parameters the plan was actually built under, so a readout never restates them
`reads`	Yes	one entry per primer in the walk: name (F1, R1, ...), sequence, strand, and the stretch it is expected to read
`primers`	Yes	just the primer sequences, in walk order, for ordering
`skipped`	Yes	anchors where no primer could be designed, each with the reason - never a silently short walk
`complete`	Yes	true when every base of the region is read at least once
`coverage`	Yes	every stretch of the region, contiguous and in order, with its depth
`authority`	Yes	the published source the read-length and dead-zone defaults come from
`readCount`	Yes	how many primers the walk needs
`doubleStranded`	Yes	true when every base is read from both directions
`singleStranded`	Yes	stretches read from one strand only, when both were asked for

Schema Changelog

Changes observed during successful MCP inspections.

First observedOct 20, 2026

TDQS

A4.2/5.0

Behavior4/5

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

Annotations declare the safety profile (readOnlyHint=false, destructiveHint=false, openWorldHint=false). The description adds real behavior beyond that: tiled reads with confirmed overlap, both-strands-by-default, and a reported coverage plus un-reachable stretches. It does not address runtime/permission behavior, keeping it below a 5.

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?

Three tight sentences, front-loaded with what the tool does and the mental model ('a WALK... not one pair'), then the use case, then default rationale. Minimal waste, though the facility-default sentence overlaps with schema text.

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?

An output schema exists, so return values need not be explained, and the description still signals that coverage and unreachable stretches are reported. Combined with annotations and a fully documented schema for a 10-parameter tool, nothing an agent needs to invoke it correctly is missing.

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 10 parameters including the rationale for read_length and dead_zone defaults. The description restates the facility-default framing ('MSU RTSF, ABI 3730XL') without adding syntax or meaning the schema lacks, so the baseline 3 applies.

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?

Specific verb+resource ('Design a WALK of sequencing primers') with scope stated precisely: tiled reads covering a whole region, not one pair. It distinguishes itself from the single-pair siblings (design_primer_pairs, design_primers) by naming that exact contrast.

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?

Frames the use case as 'how do I read all 6 kb of this construct' and explicitly states a single pair 'does not answer' it, which gives clear when-to-use context and implies the alternative. It stops short of naming design_primer_pairs directly as the excluded sibling, so it is clear but not fully explicit.

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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