jean — Molecular Biology & Genomics

browse_region

Read-only

Read one window of a genome the way a genome browser shows it: the cytogenetic bands it spans, the transcripts in the chosen RefSeq set, which residues of each protein the window encodes (translated from the assembly’s own bases), how many dbSNP 155 variants fall in it and how many ClinVar calls pathogenic, and every CRISPR site for the chosen nuclease (SpCas9 unless told otherwise) with its strand, cut position and on-target scores. Give a gene symbol (resolved through MANE Select, then HGNC) or a locus, 1-based and inclusive. Each lane refuses a window wider than it will read, and says so.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`gene`	No	a gene symbol; the window is its MANE Select (or HGNC) transcript with a 2% margin either side. Takes precedence over `locus`.
`locus`	No	the window, 1-based and inclusive, when no `gene` is given.
`_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.
`_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.
`assembly`	Yes	the UCSC assembly name (hg38, hg19, mm39…).
`nuclease`	No	which nuclease the CRISPR sites are enumerated for (its PAM and cut rule). On-target scores are SpCas9-trained and come back null for any other. Values: SpCas9 (SpCas9 · NGG), SpCas9-NG (SpCas9-NG · NG), SpG (SpG · NGN), SpRY (SpRY · NRN), xCas9 (xCas9 · NG), SaCas9 (SaCas9 · NNGRRT), SaCas9-KKH (SaCas9-KKH · NNNRRT), AsCas12a (AsCas12a · TTTV), LbCas12a (LbCas12a · TTTV), enAsCas12a (enAsCas12a · TTTV).	SpCas9
`gene_track`	No	which RefSeq set the transcripts and protein residues come from. Values: ncbiRefSeqSelect (RefSeq Select and MANE), ncbiRefSeqCurated (RefSeq Curated), ncbiRefSeq (RefSeq All), ncbiRefSeqPredicted (RefSeq Predicted).	ncbiRefSeqSelect

Output Schema

TableJSON Schema

Name	Required	Description
`sites`	Yes	CRISPR sites: spacer, PAM, strand, 1-based protospacer bounds, cut position and Rule Set 1 / CRISPRscan scores
`window`	Yes	the window read, 1-based inclusive, and how it was reached
`protein`	Yes	per transcript: accession, strand, the first and last residue numbers in the window and the residues themselves
`summary`	Yes	what each lane found in the window, generated from the run
`refusals`	Yes	each lane that did not run for this window, and why

Schema Changelog

Changes observed during successful MCP inspections.

First observedOct 20, 2026

TDQS

A3.9/5.0

Behavior4/5

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

Annotations already cover the safety profile (readOnlyHint=true, destructiveHint=false, openWorldHint=true). The description adds meaningful context beyond that: the default nuclease ('SpCas9 unless told otherwise'), the MANE/HGNC resolution chain, and the lane-level window-size limits ('Each lane refuses a window wider than it will read, and says so'). That last point is a useful behavioral disclosure.

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?

The main purpose is front-loaded in the first clause, and every subsequent clause maps to a distinct output lane, so little is wasted. It is a dense run-on paragraph rather than structured bullets, which slightly hurts scannability, but the density is justified by the tool's breadth.

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 an output schema present, return-value explanation is unnecessary, and the description still covers inputs, resolution precedence, defaults, and lane limits. For a 7-parameter, nested-schema tool it is close to complete, though it omits any note on cost, rate limits, or how the _subject/_files project context interacts with the browse.

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 coverage is 100% and the schema descriptions are already unusually rich, documenting gene precedence, 1-based inclusive locus, nuclease default, and track options. The description largely restates this ('Give a gene symbol... or a locus, 1-based and inclusive', 'SpCas9 unless told otherwise') rather than adding new parameter meaning, 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?

The description opens with a specific verb+resource ('Read one window of a genome the way a genome browser shows it') and then enumerates the exact data lanes returned (cytogenetic bands, transcripts, protein residues, dbSNP 155 counts, ClinVar pathogenic calls, CRISPR sites). This level of specificity clearly distinguishes it from siblings like annotate_region or lookup_gene.

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 explains the two input modes (gene symbol resolved through MANE Select then HGNC, or a locus) and states that gene takes precedence, which implies usage. However, it never names an alternative sibling (e.g. annotate_region, lookup_gene) or states when NOT to use this tool, so routing guidance is only implied.

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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