plant-genomics-mcp

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JASPAR: TF Binding Motifs

tf_binding_motifs

Read-onlyIdempotent

Fetch curated transcription-factor DNA binding motifs for a plant locus from JASPAR. Returns confirmed motifs with matrix IDs, TF class, assay type, IUPAC consensus, and references.

Instructions

Fetch curated transcription-factor DNA binding motifs for a locus from JASPAR (jaspar.elixir.no; free, no key) — the cis-regulatory view. Resolves the locus → UniProt accession + gene symbol, searches JASPAR by symbol scoped to the organism's taxid, then CONFIRMS each candidate by matching the accession against the profile's uniprot_ids. Returns per motif the JASPAR matrix id, TF class/family, assay type (SELEX / ChIP-seq / PBM / DAP-seq), an IUPAC consensus derived from the position-frequency matrix (e.g. CACGTG, the G-box/ABRE core), motif length, PubMed refs, and the SVG sequence_logo and JASPAR web_url — links for the client to fetch; no tool on this server retrieves them. IMPORTANT: JASPAR's name search is fuzzy, so name-similarity hits belonging to a DIFFERENT gene are returned separately in name_only_matches and must NOT be attributed to this locus; only motifs is UniProt-confirmed. found=false means the gene has no curated profile (not a TF, or its family is unprofiled for that species) — a normal outcome, not an error. Use jaspar_motif to retrieve the raw matrix for any matrix_id. Coverage is Arabidopsis-heavy (1236 profiles) and thin elsewhere (maize 131, soybean 91, wheat 58, tomato 51, rice 10; Brachypodium and sorghum have none). Defaults to arabidopsis_thaliana; pass organism= for other species.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`locus`	Yes	e.g. AT2G46830 (Arabidopsis CCA1), Os01g0100100 (rice RAP-DB)
`organism`	No	Plant organism — accepts canonical slug (arabidopsis_thaliana), scientific or common name, or NCBI taxid	arabidopsis_thaliana

Output Schema

TableJSON Schema

Name	Required	Description
`found`	Yes	True if any profile was UniProt-confirmed for this locus
`locus`	Yes
`total`	Yes	How many UniProt-confirmed JASPAR profiles exist upstream for this query, all pages (pre-cap) (#123)
`motifs`	No	UniProt-confirmed binding profiles
`tax_id`	Yes	NCBI taxid the JASPAR search was scoped to
`returned`	Yes	Rows in this payload (#123)
`accession`	Yes	Resolved UniProt accession
`truncated`	Yes	True if the motif list was capped
`motif_count`	Yes	Total confirmed profiles (pre-cap)
`upstream_version`	No	JASPAR release that produced THIS response, — always null today: this backend states no release on its responses; upstream_release(backend='jaspar') reports the release its own endpoint calls current at query time, or why there is none. null means JASPAR did not state one — never that no release exists, and never inferred from a separate metadata call, which can describe a different release than the one that answered.
`name_only_matches`	No	Name-similarity hits belonging to a DIFFERENT gene [{matrix_id, name, uniprot_ids}] — not this locus's motifs
`gene_names_searched`	No	Gene symbols used as JASPAR search keys

Schema Changelog

Changes observed during successful MCP inspections.

Changed1 schema field changedv1.27.0Sep 27, 2026

changedOutput schema / properties / upstream_version / description

Previous value: -"JASPAR release that produced THIS response, — always null today: this backend states no release on its responses. null means JASPAR did not state one — never that no release exists, and never inferred from a separate metadata call, which can describe a different release than the one that answered."New value: +"JASPAR release that produced THIS response, — always null today: this backend states no release on its responses; upstream_release(backend='jaspar') reports the release its own endpoint calls current at query time, or why there is none. null means JASPAR did not state one — never that no release exists, and never inferred from a separate metadata call, which can describe a different release than the one that answered."

Changed6 schema fields changedv1.22.0Sep 24, 2026

changedOutput schema / $defs / TfBindingMotif / properties / sequence_logo / description

Previous value: -"URL of the SVG sequence logo"New value: +"URL of the SVG sequence logo — a link for the client to open or fetch; no tool on this server dereferences it"

changedOutput schema / $defs / TfBindingMotif / properties / web_url / description

Previous value: -"JASPAR profile page"New value: +"JASPAR profile page — a link for the client to open or fetch; no tool on this server dereferences it"

addedOutput schema / properties / returned

Added value: +{
+  "description": "Rows in this payload (#123)",
+  "title": "Returned",
+  "type": "integer"
+}

addedOutput schema / properties / total

Added value: +{
+  "description": "How many UniProt-confirmed JASPAR profiles exist upstream for this query, all pages (pre-cap) (#123)",
+  "title": "Total",
+  "type": "integer"
+}

addedOutput schema / properties / upstream_version

Added value: +{
+  "anyOf": [
+    {
+      "type": "string"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "description": "JASPAR release that produced THIS response, — always null today: this backend states no release on its responses. null means JASPAR did not state one — never that no release exists, and never inferred from a separate metadata call, which can describe a different release than the one that answered.",
+  "title": "Upstream Version"
+}

changedOutput schema / required

Previous value: -[
-  "locus",
-  "accession",
-  "tax_id",
-  "found",
-  "motif_count",
-  "truncated"
-]New value: +[
+  "total",
+  "returned",
+  "locus",
+  "accession",
+  "tax_id",
+  "found",
+  "motif_count",
+  "truncated"
+]

Addedv1.18.2Jul 24, 2026

TDQS

A4.4/5.0

Behavior5/5

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

Beyond the annotations (read-only, open world, idempotent), the description discloses the multi-step resolution process, the fuzzy-name-search caveat that returns name_only_matches separately, and the fact that the SVG/web_url are links for the client to fetch because no tool on the server retrieves them. It also explicitly labels found=false as a normal outcome, adding substantial behavioral context the annotations do not carry.

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 description is dense and front-loaded with the core purpose, then methodically covers process, return contents, caveats, and coverage. It is a single long paragraph but every sentence contributes; the length is justified by the tool's complexity, though slight tightening could improve scannability.

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?

For a tool with two parameters and an existing output schema, the description covers all necessary operating context: how confirmation works, what the return includes, the meaning of found=false, the fuzzy-match caveat, the server-side vs client-side fetch distinction, and species coverage. 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?

The schema already documents both parameters with 100% coverage, including examples and the default for organism. The description reinforces the default and adds coverage context but does not materially extend parameter semantics beyond the schema, so the baseline of 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 clear verb+resource: 'Fetch curated transcription-factor DNA binding motifs for a locus from JASPAR' and distinguishes it from the sibling jaspar_motif by noting that this tool returns the motif collection plus metadata while jaspar_motif retrieves the raw matrix. It also identifies the cis-regulatory view, making the purpose unmistakable.

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?

It gives an explicit pointer to the alternative jaspar_motif for raw matrices and clarifies when found=false is expected (gene lacks a curated profile) rather than an error. It also provides coverage guidance across species, which helps the agent set expectations. It does not, however, enumerate conditions for preferring this over other locus tools, but in context the main alternative is addressed.

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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