askBrassica

Install

Pick the AI app you use, then copy the settings.

Passed 2/3 checks · What you ask goes through the maker’s server (askbrassica.plantdatabases.org) · ✓ Commands checked Nov 14, 2026

claude mcp add --transport http --scope user askbrassica https://askbrassica.plantdatabases.org/mcp

{
  "mcpServers": {
    "askbrassica": {
      "url": "https://askbrassica.plantdatabases.org/mcp"
    }
  }
}

{
  "servers": {
    "askbrassica": {
      "type": "http",
      "url": "https://askbrassica.plantdatabases.org/mcp"
    }
  }
}

Which apps can use it

Based on how this server connects and on each app’s own docs, checked Nov 10, 2026.

Connect over the internet in

ClaudeChatGPTGooseLM StudioMsty StudioCherry StudioCursorVS Code + GitHub CopilotVisual StudioWindsurf (Devin Desktop)ZedKiroClineContinueJetBrains AI AssistantClaude CodeCodex CLIGemini CLIOpenCodenodecodeWarpLibreChatOpen WebUIRaycast

All apps, with pros and cons →

What it can do

Tool names and descriptions exactly as the server reported them on Nov 14, 2026. The maker wrote them, not us; we show them as plain text.

• search_data

  Full-text search across all askBrassica resources (genes, germplasm, genotyping datasets, files). Filters (exact values): database e.g. 'Ensembl Plants', 'Brassica Genome (brassicagenome.net)', 'GBIF genebank accessions'; entry_type e.g. 'Gene annotation', 'Germplasm', 'Genotypin

• find_germplasm

  Find Brassica genebank accessions by accession number or name: Brassica, Camelina, Sinapis and Raphanus accessions from GBIF, with the holding genebank (FAO WIEWS code) and accession number; mostly Svalbard Global Seed Vault safety duplicates. Passport data are minimal (no traits

• data_sources

  What askBrassica currently indexes: record counts per database and data type, and data versions.

• find_gene

  Look up a gene by Ensembl gene ID or gene name/symbol in Ensembl Plants: species, location, assembly, biotype, description and link. Names are searched in all of: brassica_napus, brassica_rapa (Chiifu), brassica_rapa_ro18 (R-o-18), brassica_rapa_z1 (Z1), brassica_oleracea, brassi

• genes_in_region

  Genes overlapping a region of one Ensembl Plants genome (max 5 Mb). species is an Ensembl name, e.g. 'brassica_rapa' (chromosomes A01-A10) or 'brassica_oleracea' (C1-C9); chromosome names as in that assembly. Brassica napus is scaffold-level in Ensembl Plants (Darmor-bzh v4.1), s

• orthologues

  Orthologues of a gene from Ensembl Plants Compara (gene trees across plant genomes), e.g. the Brassica copies of an Arabidopsis gene. gene: Ensembl ID or name; target_species: Ensembl name to restrict to (e.g. 'brassica_napus'). Returns orthologue IDs, species, relationship (one2

• pangenome_gene

  Presence/absence of a gene across the accessions of a crop pangenome: how many accessions carry it, core or variable, which accessions lack it (and which carry it, if fewer), location, description and genome browser link. gene: a pangenome gene ID, a B. napus Ensembl (Darmor-bzh

• pangenome_region

  Pangenome genes in a region (max 5 Mb) with how many accessions carry each, e.g. to see which genes in a QTL interval show presence/absence variation. chromosome like 'A01' or 'chrA01'. Datasets: 'bnapus' = B. napus pangenome (Darmor-bzh v8.1 plus 52 accessions, 94,013 genes; IDs

• pangenome_compare

  Genes whose presence frequency differs most between two groups of pangenome accessions (accession names from pangenome_accessions, 'form: ' selectors such as 'form:Synthetic' or 'form:cauliflower', or ['all']). min_diff is the minimum absolute frequency difference (0-1); positive

• pangenome_accessions

  Accessions in a crop pangenome with their metadata (form, genotype code, synthetic parents where known) and the number of genes each carries and lacks. dataset defaults to the first one. Datasets: 'bnapus' = B. napus pangenome (Darmor-bzh v8.1 plus 52 accessions, 94,013 genes; ID

• arabidopsis_function

  Function of a gene through its Arabidopsis thaliana orthologue(s): Ensembl Plants Compara orthologues, then UniProtKB curated function, protein and gene names, mutant (disruption) phenotype, subcellular location and GO terms. gene: an Ensembl gene ID or name of any crop genome he

• resistance_loci

  Curated resistance loci of Brassica crops: blackleg (Leptosphaeria maculans: Rlm1-Rlm14, LepR1-3, RlmS), clubroot (Plasmodiophora brassicae: CRa, CRb, Crr1-5, Rcr1-10, PbBa...), and in Brassica vegetables downy mildew (BraDM, Pp523, BoDMR2...), Fusarium yellows (FocBo1, Foc-Br1),

• resistance_gene_analogues

  Resistance gene analogues (RGAs) in the B. napus pangenome (1,749 genes: NBS-LRR classes TNL, CNL, RNL, NL, TN, CN, RN, NBS, TX; receptor-like kinases RLK; receptor-like proteins RLP), with presence/absence across the 53 pangenome accessions, description and location (Darmor-bzh

• bnir_gwas

  Genome-wide association peaks for B. napus traits from BnIR (HZAU): 135 traits from 10 GWAS studies (seed oil fatty acids and erucic acid, glucosinolates, oil content, flowering time, plant height, branching, silique and seed traits, cadmium, salt and other stress responses...).

• bnir_expression

  B. napus (ZS11) RNA-seq expression in TPM from BnIR: 'stress' (leaf and root time courses, 0.25-24 h, under salt, drought, osmotic, heat, cold 4 C and freezing -4 C, with controls at the same time points), 'hormone' (leaf and root, IAA, ACC, GA, ABA, trans-zeatin, JA, brassinolid

• expression_experiments

  Brassica RNA-seq experiments held by askBrassica (Expression Atlas and SRA study SRP159041 (B. napus leaf cold, heat and drought; quantified by askBrassica)): baseline (TPM by tissue / developmental stage / treatment) and differential (stress, pathogen, genotype contrasts). query

• gene_expression

  Where and when a Brassica gene is expressed, and under which treatments it changes, from Expression Atlas and SRA study SRP159041 (B. napus leaf cold, heat and drought; quantified by askBrassica). gene: Ensembl gene ID (e.g. GSBRNA2T00000001001 for B. napus, Bra000001 for B. rapa

• expression_genes

  Genes characteristic of a tissue/stage or responsive to a treatment in one Expression Atlas experiment. Baseline experiment + group (text matched to group labels, e.g. 'root', 'grain'): genes with TPM >= min_tpm in a matching group ranked by specificity = (max TPM in matching gro

• snp_lines

  Find SNP-genotyped lines in CropSNPdb by name or AGG accession (e.g. 'Westar', 'Darmor'). Returns line name, accession(s), country, pedigree, status, breeding organisation and donor. dataset: 'Brassica napus Darmor v81' (default, 459 lines), 'Brassica napus Darmor v41', 'Brassica

• snp_genotypes

  SNP genotype calls for up to 50 lines in a region (chromosome like 'A01'). Returns markers with positions and each line's call. Keep regions small (a few Mb) for many lines.

• snp_compare_lines

  Compare two lines' SNP genotypes on a chromosome (optionally a region): markers compared, identical, different, % identity and the regions where they differ (useful for pedigree/introgression questions).

• snp_haplotype_carriers

  Lines that share a reference line's SNP haplotype in a region (max 5 Mb), e.g. which genebank lines carry the Westar haplotype around a gene. Only markers polymorphic in the panel (minor allele frequency >= min_maf) are used, and a match needs calls at >= min_called of them with

• snp_markers

  SNP array markers (IDs and positions) in a region, with the total count.

• snp_phenotypes

  Field trial trait data held in CropSNPdb for this crop (T3 trials with Crop Ontology trait IDs, Australian Grains Genebank records). With no arguments, lists the available traits. Filter by line and/or trait: trait matches the exact name or any part of it (e.g. 'Height', 'grain y

• search_literature

  Search publications and preprints in Europe PMC (PubMed, PMC, bioRxiv and others). query: free text or Europe PMC syntax (e.g. 'grain size QTL 6A', 'TITLE:"pan-genome"'). gene: optional gene name or Ensembl ID; its curated synonyms and RefSeq IDs are OR-ed into the query (e.g. ge

• get_paper

  Full record for one paper: DOI (10.xxxx/..), PMID (digits) or PMCID (PMC...). Returns the abstract, open-access status and full-text links.

• brapi_germplasm_studies

  Phenotyping studies (field and glasshouse trials) with trait data for a Brassica line, live from the BrAPI nodes (currently the INRAE Brassica trials in GnpIS (rapeseed and cabbage collections), served through FAIDARE). germplasm: a cultivar or line name (matched exactly; upper/t

• brapi_observations

  Trait observations for a Brassica line from the BrAPI nodes (currently the INRAE Brassica trials in GnpIS (rapeseed and cabbage collections), served through FAIDARE), summarised per study and variable: n, mean, min, max (numeric values) or the distinct values, season and location

• gene_pathways

  Plant Reactome metabolic and signalling pathways of a gene (Gramene), with the top-level category and a link to the pathway diagram. gene: an Ensembl Plants gene ID or a gene name/symbol. Pathways are projected from rice by orthology, so say they are inferred. Use pathway_genes f

• pathway_genes

  Genes in a Plant Reactome pathway: pathway is a name or words from it ('jasmonic acid biosynthesis', 'gibberellin', 'flavonoid') or a stable ID (R-TAE-1119332). species: a species name as Plant Reactome writes it ('Triticum aestivum', 'Brassica napus', 'Glycine max'); default all

• trait_hits

  Trait-associated positions across the genome for a chromosome overview: GWAS marker-trait associations and peaks, named trait genes and mapped trait loci held by this site, with chromosome sizes, each with a genome browser link where the assembly is loaded. trait: words to match

• brassica_gene_view

  Interactive gene view for one Brassica gene: a relationship map of its orthologues in B. rapa, B. oleracea, B. juncea, Camelina and Arabidopsis, Arabidopsis function, presence/absence across the B. napus (53 accessions) or B. oleracea (10) pangenome by crop form, BnIR stress resp

Basic checksi

We check information anyone can see; we have not read the code. Checks that do not apply are left out of the count. · Checked Nov 14, 2026

• ! Caution

  Maker matches the repo

  The registry lists no source repo, so we cannot match the publisher (plantdatabases.org) to the code

• … Not checked yet

  Still maintained

  We have not read this repo from GitHub yet

• … Not checked yet

  Has a licence

  We have not read this repo from GitHub yet

• ✓ Pass

  Endpoint responds

  Responded in 798 ms (HTTP 200)

• – Not applicable

  Sign-in with OAuth

  No sign-in needed

• ✓ Pass

  No hidden instructions in tool descriptions

  Read 32 tool descriptions and found no hidden instructions to the AI

User reviews

No reviews yet

Sign in with Google to write a review

Compared with others in Search & AI memoryi

• More stars than 0% of the other 6096 servers in this category
• Published to the registry more recently than 99% of the other 6096 servers in this category
• Basic checks equal to or better than 50% of the other 6096 servers in this category

Compared with every active server in this category in the registry. Stars count only when the publisher owns the repo.

Others in the same category

Servers in the same category from other makers, sorted by stars.

Reading a card:↓ Downloads per weeki★ GitHub starsiThree pillars: reviews · checks · usageiUpdated = latest version published to the registryi

Context7

Feeds AI the latest docs for libraries and frameworks before it answers, so code it writes does not use outdated, removed functions.

by upstash·Widely used·↓ 1.2M/wk·★ 64.8K·Updated 2 days ago

Computer or cloud

Install

Codebase Memory

Codebase knowledge graph for AI agents — 162 languages, sub-ms queries, 99% fewer tokens.

by DeusData·Widely used·↓ 16.8K/wk·★ 48.6K·Updated 28 days ago

Runs on your computer

Install

OpenSEO

Keyword research, site audits, rank tracking and AI visibility for your AI agent.

by every-app·Widely used·★ 27.6K·Updated today

Runs in the cloud✓ everyapp.com

How to connect

README from the maker

No README found in the repo