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Ucsc Genome

by io.github.pipeworx-io
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Ucsc Sequence

ucsc_sequence
Read-onlyIdempotent

"What is the DNA sequence at [chr:start-end]" / "get the reference bases for [region] in hg38" / "pull the sequence around [variant position]" — AUTHORITATIVE reference DNA for a genomic interval from the UCSC assembly, returned as a plain base string with its GC content. Use it to check what the reference allele actually is at a position, to extract primer/probe context, or to pull a promoter or exon sequence. The assembly argument is required because the same coordinates return different bases in hg19 and hg38.

Input Schema

NameRequiredDescriptionDefault
endYesEnd position, 0-based and EXCLUSIVE (so end - start = length in bases).
chromYesChromosome in UCSC naming, e.g. "chr7", "chrX". The "chr" prefix is required.
startYesStart position, 0-BASED and inclusive. The Genome Browser UI and most papers are 1-based, so subtract 1 from a position you copied out of the browser location box.
genomeYesREQUIRED. UCSC assembly ID — the genome build your coordinates are in. Human: "hg38" (= GRCh38, current) or "hg19" (= GRCh37, what most older papers, dbSNP dumps and clinical spreadsheets use). Mouse: "mm39"/"mm10". These are DIFFERENT coordinate systems: the same chrom/start/end is valid in every build, so a wrong build returns confident annotations for a different gene instead of an error. Call ucsc_genomes to list the assembly IDs for a species.
revCompNoReturn the reverse complement — for a gene on the minus strand, this is the sense strand. Default false.

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4.1/5.0
Behavior4/5

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

Annotations already declare readOnly/idempotent/non-destructive, but the description adds real context beyond them: the return value (base string with GC content) and the failure mode of an unset or wrong build silently returning confident bases for the wrong locus. It does not discuss rate limits or sequence-length limits.

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?

Query-shaped openers front-load the trigger conditions, followed by the authoritative-source framing and the assembly caveat. Three sentences, each doing work; slightly dense but no filler.

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 no output schema, the description does the needed job of stating what comes back (base string plus GC content) and why the build argument cannot be omitted. For a 5-parameter read tool it is essentially complete; only inter-tool boundaries with the UCSC sibling tools are left implicit.

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 parameter descriptions are already detailed (0-based start, exclusive end, chr prefix, hg19/hg38 divergence, revComp as minus-strand sense). The description's note that assembly is required because the same coordinates differ between hg19 and hg38 restates what the schema already spells out, so it adds emphasis rather than new semantics — baseline 3.

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?

States a specific verb and resource — pull AUTHORITATIVE reference DNA for a genomic interval from the UCSC assembly — and states the return shape (plain base string plus GC content). The user-phrasing examples bracket the intent sharply enough that an agent can distinguish this from assembly-listing or track-data siblings without opening a schema.

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?

Gives concrete use cases: verifying the reference allele at a position, extracting primer/probe context, pulling promoter or exon sequence. It does not explicitly exclude or name alternative tools (e.g. when track/annotation data rather than bases is wanted), so it is clear context without routing exclusions.

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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