Categories › Knowledge & Everyday › Science: biology, chemistry, physics & engineering
Brassica and canola genes, pangenomes, stress expression, genotypes, germplasm and papers
Remote server: your requests and data go to askbrassica.plantdatabases.org. Claude Code: claude mcp add --transport http askbrassica https://askbrassica.plantdatabases.org/mcp · Claude app: Settings → Connectors → Add custom connector.
The tools this server listed when we connected to it, in its own words.
search_data — Full-text search across all askBrassica resources (genes, germplasm, genotyping datasets, files). Filters (exact values): database e.g. 'Ensfind_germplasm — Find Brassica genebank accessions by accession number or name: Brassica, Camelina, Sinapis and Raphanus accessions from GBIF, with the holdidata_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 agenes_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) oorthologues — Orthologues of a gene from Ensembl Plants Compara (gene trees across plant genomes), e.g. the Brassica copies of an Arabidopsis gene. gene: 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 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 pangenome_compare — Genes whose presence frequency differs most between two groups of pangenome accessions (accession names from pangenome_accessions, 'form:<fopangenome_accessions — Accessions in a crop pangenome with their metadata (form, genotype code, synthetic parents where known) and the number of genes each carriesarabidopsis_function — Function of a gene through its Arabidopsis thaliana orthologue(s): Ensembl Plants Compara orthologues, then UniProtKB curated function, protresistance_loci — Curated resistance loci of Brassica crops: blackleg (Leptosphaeria maculans: Rlm1-Rlm14, LepR1-3, RlmS), clubroot (Plasmodiophora brassicae: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-libnir_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, gbnir_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, coexpression_experiments — Brassica RNA-seq experiments held by askBrassica (Expression Atlas and SRA study SRP159041 (B. napus leaf cold, heat and drought; quantifiedgene_expression — Where and when a Brassica gene is expressed, and under which treatments it changes, from Expression Atlas and SRA study SRP159041 (B. napus expression_genes — Genes characteristic of a tissue/stage or responsive to a treatment in one Expression Atlas experiment. Baseline experiment + group (text masnp_lines — Find SNP-genotyped lines in CropSNPdb by name or AGG accession (e.g. 'Westar', 'Darmor'). Returns line name, accession(s), country, pedigreesnp_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 regionssnp_compare_lines — Compare two lines' SNP genotypes on a chromosome (optionally a region): markers compared, identical, different, % identity and the regions wsnp_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 genesnp_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 nosearch_literature — Search publications and preprints in Europe PMC (PubMed, PMC, bioRxiv and others). query: free text or Europe PMC syntax (e.g. 'grain size Qget_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 Brassibrapi_observations — Trait observations for a Brassica line from the BrAPI nodes (currently the INRAE Brassica trials in GnpIS (rapeseed and cabbage collections)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: apathway_genes — Genes in a Plant Reactome pathway: pathway is a name or words from it ('jasmonic acid biosynthesis', 'gibberellin', 'flavonoid') or a stabletrait_hits — Trait-associated positions across the genome for a chromosome overview: GWAS marker-trait associations and peaks, named trait genes and mappgenes_with_annotation — Find genes by function: GO term, InterPro or Pfam domain (accession or words, e.g. 'NB-ARC', 'IPR002182', 'GO:0009414', 'disease resistance'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. 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 abstannotate_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, Plblast_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 ZS11brassica_gene_view — Interactive gene view for one Brassica gene: a relationship map of its orthologues in B. rapa, B. oleracea, B. juncea, Camelina and ArabidopNot tested by KitScout yet. When our harness runs it, pros, cons and the tasks we tried appear here, with the date and evidence.