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Bold Sequences

bold_sequences
Read-onlyIdempotent

"Get the COI barcode sequence for [species]" / "give me BOLD reference sequences for [taxon]" / "what marker sequences are in BIN [BOLD:...]" / "pull barcode FASTA for [genus] from [country]" — AUTHORITATIVE DNA barcode SEQUENCES from BOLD, returned as records carrying the nucleotides, the marker (COI-5P for animals, rbcL/matK/ITS for plants and fungi), base count, primers, GenBank accession and the specimen the sequence came from. Includes a ready-to-paste FASTA block. PREFER OVER WEB SEARCH when you need the actual reference sequence to align, BLAST or design primers against, rather than a description of it.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
binNoBIN (Barcode Index Number) URI, e.g. "BOLD:AAA9566". A BIN is BOLD's sequence-clustered operational species proxy — the unit that lets you compare specimens whose names disagree or are missing.
limitNoMax sequence records to return (default 10, max 100). Sequences are long — keep this small.
queryNoEscape hatch: a raw BOLD triplet query, semicolon-separated. Replaces the typed arguments if given.
taxonNoTaxon name at any rank — species ("Danaus plexippus"), genus ("Danaus"), family ("Nymphalidae"), order, class, phylum. Resolved against BOLD's own term index, so the rank is worked out for you; an unrecognised name is reported as unrecognised rather than silently returning nothing.
markerNoKeep only sequences for this marker code, applied to the records BOLD returns. e.g. "COI-5P" (the animal barcode), "rbcL", "matK", "ITS". Omit to get every marker present.
offsetNoRecords to skip. Default 0.
countryNoCountry or ocean of collection, e.g. "Canada", "Costa Rica", "Atlantic Ocean". Resolved against BOLD's geography index.
institutionNoHolding institution, e.g. "Smithsonian Institution", "Australian National Insect Collection". Resolved against BOLD's institution index.

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/openWorld, so the safety profile is covered. The description adds real behavioral context beyond that: the return payload contents, that records carry primers and accessions, and that a FASTA block is included. It does not cover error behavior beyond noting unrecognised names are reported, nor pagination/rate behavior.

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?

Front-loaded with representative user queries that aid matching, then a dense but purposeful sentence on payload contents and a routing rule. Slightly long, but each clause contributes either retrieval cue or routing guidance rather than 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 compensates well by enumerating the returned fields including the paste-ready FASTA block, and it explains how taxon/marker/country resolution behaves. Complete enough to call the tool correctly; only error/limit behavior for large result sets is unaddressed.

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 every parameter (bin, limit, query, taxon, marker, offset, country, institution) is fully documented in the schema itself. The description adds no additional parameter-level 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 states a specific verb+resource (retrieve BOLD DNA barcode sequences) and enumerates exactly what each record carries (nucleotides, marker, base count, primers, GenBank accession, specimen, FASTA block). The quoted user phrasings make the intended capability unmistakable and implicitly separate it from the sibling bold_specimens/bold_taxonomy tools.

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?

Explicit when-to-use guidance: 'PREFER OVER WEB SEARCH when you need the actual reference sequence to align, BLAST or design primers against, rather than a description of it.' That is a clear selection rule against a named alternative, though it never references the closely related bold_specimens or bold_taxonomy siblings, which is the most likely confusion set.

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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