askBrassica

Connect Remote server

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

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

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

Settings > Connectors > Add custom connector
URL: https://askbrassica.plantdatabases.org/mcp

Tools 37 found in our last check

• 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', 'Genotypi…

• 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 trait…

• 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, brass…

• 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),…

• 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 (one…

• 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; ID…

• pangenome_compare

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

• 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; I…

• 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 h…

• 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, brassinoli…

• 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). quer…

• 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. rap…

• 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 gr…

• 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', 'Brassic…

• 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…

• 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. g…

• 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/…

• 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 locatio…

• 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…

• 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 al…

• 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…

• genes_with_annotation

  Find genes by function: GO term, InterPro or Pfam domain (accession or words, e.g. 'NB-ARC', 'IPR002182', 'GO:0009414', 'disease resistance', 'MADS-box') or Plant Reactome pathway ('gibberellin biosynthesis', R-TAE-...; kind='pathway'). kind: GO, InterPro, Pfam or pathway (defau…

• gene_neighbourhood

  Gene neighbourhood (microsynteny): the gene and its flanking genes, with their orthologues in related genomes (B. napus, B. rapa R-o-18, B. oleracea, Camelina, Arabidopsis) from Ensembl Compara. For each target genome, the collinear block holding most orthologues of the neighbou…

• gene_papers

  Papers mentioning a gene: Europe PMC search for its gene IDs (all versions, in open-access full text) and its name/symbols (in title or abstract, with Brassica/canola/rapeseed/Camelina). Each paper says whether it matched an ID or a name. Name matches can be another gene with th…

• annotate_genes

  Annotate a list of genes (up to 500 IDs or names) in one call: resolved ID, species, location, name, top InterPro/Pfam domains, GO terms, Plant Reactome pathways and orthologues in the main related genomes (['brassica_napus', 'brassica_rapa_ro18', 'brassica_oleracea', 'camelina_…

• blast_sequence

  BLAST a DNA or protein sequence (raw or FASTA; up to 20 kb DNA or 5,000 aa) against this site's databases: B. napus Darmor-bzh v4.1 and ZS11, B. oleracea TO1000 and B. rapa Chiifu genomes; CDS and proteins of the three Ensembl genomes. The program is chosen from the query and da…

• 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 res…

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