askWheat

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

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

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

{
  "servers": {
    "askwheat": {
      "type": "http",
      "url": "https://askwheat.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.

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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 askWheat resources (genes, germplasm, genotyping datasets, files). Filters (exact values): database e.g. 'Ensembl Plants', 'Watkins Wheat Pangenome', 'CropSNPdb', 'GBIF genebank accessions'; entry_type e.g. 'Gene annotation', 'Germplasm', 'Genotyping E

• find_germplasm

  Find wheat accessions/cultivars/lines by name or accession ID across five indexed sources: CropSNPdb (SNP-genotyped lines, incl. all Australian Grains Genebank wheat and CAIGE breeding lines), the Watkins Wheat Pangenome (sequenced landraces), OzWheat (CSIRO GWAS panel lines), FA

• data_sources

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

• resolve_gene

  Resolve a wheat gene symbol (e.g. Lr34, Rht-B1) or IWGSC gene ID in any RefSeq version (v1.0 TraesCS..01G, v1.1 TraesCS..02G, v2.1 TraesCS..03G, CSS2014 Traes_..) to all versions, genomic locations, curated symbol/trait (with verification status), Watkins pangenome presence and l

• gene_function

  IWGSC RefSeq v2.1 functional annotation (InterPro, Pfam, Gene Ontology) for a gene symbol or any-version IWGSC ID. annotation_types filters e.g. ['Gene Ontology'] or ['Pfam','InterPro'].

• genes_in_region

  List IWGSC genes overlapping a region. chromosome like '7D'; assembly 'v2.1' (RefSeq v2.1 coordinates) or 'v1.0' (RefSeq v1.0 coordinates, v1.1 gene IDs). Region size is capped at 20 Mb.

• find_marker

  Position(s) of a genetic marker (90K/80K/9K iSelect, 35K Axiom, KASP, DArT, SSR e.g. 'BS00000713', 'wmc617', 'Xgwm149'; 40K array IDs such as 'IWB61980' or 'AVRIG14047' come from CropSNPdb) on IWGSC RefSeq v2.1 (IWGSC GMAP alignments), with genes within +/- flank bp of each hit.

• wheat_homologues

  Homoeologues (the A/B/D copies), and orthologues in other grasses and Arabidopsis, of a bread wheat gene from Ensembl Plants Compara gene trees. gene: symbol or any IWGSC ID (converted to RefSeq v1.1). By default orthologues are listed for durum and wild emmer, T. urartu, Ae. tau

• wheat_mutants

  Induced mutations and natural variants in and around a bread wheat gene. source 'ems' (default): EMS mutant lines of tetraploid Kronos and hexaploid Cadenza with exome-capture sequencing (Krasileva et al. 2017; 2,735 lines), giving the line ID to order, e.g. Cadenza1158; 'diversi

• wheat_variants_in_region

  EMS mutations and exome-capture variants in a bread wheat interval on IWGSC RefSeq v1.0, including intergenic ones (promoters, unannotated regions, off-target capture). region: 'chr:start-end', e.g. '3A:100000000-100500000' (max 5 Mb). source 'ems', 'diversity' or 'all' (default)

• wheat_mutant_line

  Every mutation Ensembl lists for one EMS line (Cadenza or Kronos exome-capture TILLING; Krasileva et al. 2017), e.g. 'Cadenza1166' or 'Kronos2235': counts by consequence, the genes with truncating mutations, and the mutations (gene, consequence, amino-acid change, RefSeq v1.0 pos

• wheat_knockout_screen

  Which genes have EMS alleles in every homoeologue, i.e. can be knocked out across A, B and D by crossing Cadenza/Kronos lines. For each gene (genes: up to 300 symbols or IWGSC IDs, or region: RefSeq v1.0 interval up to 10 Mb, e.g. a QTL) the A/B/D copies come from Ensembl Compara

• watkins_gene_presence

  Presence/absence of one gene across the 1,038 Watkins pangenome accessions: present count, core/variable, counts by ancestral group (AG1-AG7, Modern), continent and growth habit, UniProt/GO annotation and links. gene: symbol, any IWGSC RefSeq ID, or a pangenome gene-model ID.

• watkins_gene_accessions

  Watkins accessions that carry (present=True) or lack (present=False) a gene, optionally filtered by country, continent, ancestral_group (AG1-AG7 or Modern) or growth_habit. Returns metadata, coordinates and Seedstor ordering links.

• watkins_compare_groups

  Genes whose presence frequency differs most between two sets of Watkins accessions. group_a / group_b as ' : ' with field one of group (ancestral group), country, continent, growth_habit, e.g. 'group:AG3' vs 'group:Modern', 'country:India' vs 'country:China'. min_diff is the mini

• watkins_find_genes

  Find Watkins pangenome genes by UniProt protein name, gene name, protein family or ID fragment (e.g. 'FAR1', 'NLR', 'Disease resistance protein RGA'). Returns gene IDs with UniProt/GO annotation.

• watkins_accession

  One Watkins accession (e.g. WATDE0063, or a synonym): origin, ancestral group, coordinates, Seedstor link, number of genes present, presence/absence of the listed genes (symbols or any IWGSC IDs accepted), all its phenotype records (trial, trait, value, units) and any RIL populat

• watkins_phenotypes

  Field/glasshouse phenotypes of Watkins accessions (heading, height, grain size/weight/quality, senescence, lodging, rust and mildew scores, morphology). With no arguments, lists the trials (JIC UK 2006-2020, Egypt 2019-2021, Limagrain seedling yellow rust 2020, Kenya/Ethiopia rus

• watkins_gene_trait

  Compare a trait between Watkins accessions that carry vs lack a gene, per trial: n, mean and median per group and a Mann-Whitney p-value (exploratory; no correction for population structure). gene: symbol, any IWGSC RefSeq ID or pangenome gene-model ID. trait: exact name from wat

• watkins_populations

  Paragon x Watkins (and a few Robigus/other x Watkins) RIL populations: Watkins parent, country, ancestral group, number of RILs, GRU seed code, genetic map type and whether it donated TK-NILs. With population (e.g. 'ParW034') or watkins_parent (e.g. 'WATDE0005') also lists the tr

• watkins_population_phenotypes

  Trial phenotypes (line means per trial) of Paragon x Watkins RILs and TK-NILs: heading, height, yield, grain traits, biomass, N content and more from JIC, Rothamsted and Nottingham trials (2011-2022). population_type 'RIL', 'NIL' or 'check' (parents and controls, e.g. Paragon). l

• watkins_trait_genes

  Which variable genes differ in presence between Watkins accessions with high vs low values of a trait in one trial (e.g. late vs early heading). Accessions are split into top/bottom quartile (split: quartile, tercile, median) within each ancestral group (stratify_by_group) and ev

• watkins_nil_genes

  Genes inside the Watkins introgression of a TK-NIL (Watkins segment in a Paragon background), with presence in the Watkins donor and frequency in modern cultivars and landraces. nil_line is a NIL line name from watkins_population_phenotypes (e.g. 'ParW141_0016-7-10-Q2D-Hd-P'). Th

• watkins_gene_haplotypes

  Haplotypes of a gene across the Watkins landraces and modern cultivars (WatSeq, 1,051 accessions). 'snp' (default where built): accessions grouped by their SNP alleles in the gene +-2 kb (MAF >= 0.02), each haplotype with its coding changes (e.g. p.Arg134Gln), whether it is Chine

• watkins_haplotype_trait

  Trait values per haplotype of a gene (watkins_gene_haplotypes) in each Watkins trial: n, mean and median per haplotype and a Kruskal-Wallis test across haplotypes with >= min_n accessions. Exploratory: no correction for population structure or multiple testing, so a difference ca

• watkins_lof_alleles

  Watkins landraces and modern cultivars carrying a predicted loss-of-function allele of a gene (WatSeq, 1,051 accessions): each stop-gained, start/stop-lost or splice-site SNP with its protein change, the number of homozygous and heterozygous carriers, and the carriers (accession,

• watkins_accession_lof

  Genes with a predicted loss-of-function allele (stop gained, start/stop lost, splice site) in one Watkins landrace or modern cultivar (WatSeq). accession: Watkins store code or WatSeq sample name (e.g. 'Watkins 1190027', 'WATDE0027', 'Paragon'). genes optionally restricts to a ge

• expression_experiments

  Bread wheat RNA-seq experiments held by askWheat (Expression Atlas and SRA study SRP045409 (seedling drought, heat and combined stress; quantified by askWheat)): baseline (TPM by tissue / developmental stage / treatment) and differential (stress, pathogen, genotype contrasts). qu

• gene_expression

  Where and when a wheat gene is expressed, and under which treatments it changes, from Expression Atlas and SRA study SRP045409 (seedling drought, heat and combined stress; quantified by askWheat). gene: symbol or any IWGSC RefSeq ID (converted to v1.1, as used by Atlas). Baseline

• 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

• wheat_homoeologue_expression

  Relative expression of a wheat gene's A, B and D homoeologues per tissue/stage (Expression Atlas baseline experiments), with the homoeologue expression balance category of each tissue: balanced, A/B/D dominant or A/B/D suppressed, by distance to the ideal proportions (Ramirez-Gon

• snp_lines

  Find SNP-genotyped lines in CropSNPdb by name or AGG accession (e.g. 'Cadenza', 'AGG 38862', 'CAIGE ZWB17' or a CAIGE GID '7396745'). Returns line name, accession(s), country, pedigree, status, breeding organisation and donor. dataset: 'wheat40k' (default) or 'wheat90k'.

• snp_genotypes

  SNP genotype calls for up to 50 lines in a region (chromosome like '2D'). 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 Cadenza 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

• ozwheat_mtas

  Marker-trait associations from the OzWheat GWAS (285 Australian and international wheat cultivars and lines; glasshouse 2016 and field trials at Canberra 2018-19, Wagga 2018, Narrabri 2019). Traits: days to anthesis, days to heading, degree-days to heading ('flowering'/'heading')

• ozwheat_lines

  OzWheat diversity panel lines (285 Australian and international cultivars and breeding lines): name, OzWheat ID, Australian Grains Genebank (AGG) accession, pedigree and phenotype BLUEs (days to anthesis/heading, degree-days to heading, height per trial). query matches name, OzWh

• genebank_phenotypes

  Field phenotypes of wheat cultivars and genebank accessions from IPK e!DAL (CC BY 4.0). Datasets: 'GABI-WHEAT' (372 European elite cultivars 1975-2007; 16 traits incl. grain yield, heading, height, TKW, protein, sedimentation, falling number, FHB, Septoria, tan spot; BLUEs per tr

• brapi_germplasm_studies

  Phenotyping studies (field and glasshouse trials) with trait data for a wheat line, live from the BrAPI nodes (currently the INRAE wheat trial network and Whealbi trials in GnpIS, served through FAIDARE). germplasm: a cultivar or line name (matched exactly; upper/title case are t

• brapi_observations

  Trait observations for a wheat line from the BrAPI nodes (currently the INRAE wheat trial network and Whealbi trials in GnpIS, served through FAIDARE), summarised per study and variable: n, mean, min, max (numeric values) or the distinct values, season and location. germplasm: li

• wheat_gene_catalogue

  Catalogue of Gene Symbols for Wheat (McIntosh et al., GrainGenes; 2024 edition): the official register of designated wheat genes and alleles. query: a gene or allele symbol ('Lr34', 'Rht-B1b'), locus ('Rht-B1' lists all its alleles), old synonym ('Rht1', 'Ppd1', 'NAM-B1'), trait

• 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 symbol or IWGSC 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.

• 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

• wheat_gene_view

  Interactive gene view for one bread wheat gene: a relationship map of its A/B/D homoeologues, orthologues (durum, Ae. tauschii, barley, rice, maize, Arabidopsis and others), EMS knockout lines per copy, Watkins haplotypes, expression responses and recent papers, with tabs for mut

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 857 ms (HTTP 200)

• – Not applicable

  Sign-in with OAuth

  No sign-in needed

• ✓ Pass

  No hidden instructions in tool descriptions

  Read 49 tool descriptions and found no hidden instructions to the AI

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