askPulse

Connect Remote server

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

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

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

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

Tools 28 found in our last check

• search_data

  Full-text search across all askPulse resources (genes, germplasm, genotyping datasets, files). Filters (exact values): database e.g. 'Ensembl Plants', 'Legume Information System', 'GBIF genebank accessions'; entry_type e.g. 'Gene annotation', 'Germplasm', 'Genotyping Experiment'…

• find_germplasm

  Find pulse and legume genebank accessions by accession number or name (e.g. 'ICC 4958' for chickpea at ICRISAT): chickpea, lentil, pea, faba bean, lupin, grass pea, Phaseolus, Vigna, pigeonpea, soybean, peanut and Medicago accessions from GBIF, with the holding genebank (FAO WIE…

• data_sources

  What askPulse 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: pisum_sativum (Cameor v1a), pisum_sativum_gca024323335v2gb (pea ZW6), pisum_sativum_gca964186695v1gb (pea JI2822), v…

• genes_in_region

  Genes overlapping a region of one Ensembl Plants genome (max 5 Mb). species is an Ensembl name, e.g. 'pisum_sativum', 'vicia_faba', 'glycine_max' or 'lupinus_angustifolius'; chromosome names as in that assembly. Chromosome names differ by assembly: pea 1LG6..7LG7, narrow-leafed…

• 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. 'medicago_truncatula' or 'pisum_sativum'). Returns orthologue IDs, sp…

• 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…

• legume_gene

  Chickpea or lentil gene from the Legume Information System (these genomes are not in Ensembl Plants): location, functional description, LIS legume gene family and link. gene: a gene ID (e.g. 'Ca1g000100', 'Lcu.2RBY.1g000010') or words from the description (e.g. 'flowering locus…

• legume_pangene

  The same gene across chickpea or pea assemblies and annotation versions, from LIS pangene sets (synteny-aware clustering). Chickpea (Cicer.pan3): kabuli CDC Frontier v3 (Ca1g000200), v1/v2 (Ca_00003), desi ICC 4958 (Ca_) and wild C. reticulatum (Cr1g…) and C. echinospermum (Ce…)…

• legume_genes_in_region

  Chickpea or lentil genes in a region (max 5 Mb) with descriptions and gene families. dataset 'chickpea' (CDC Frontier v3, chromosomes chr1-chr8), 'chickpea_kabuli_v1' (UWA kabuli v2.6.3, Ca1-Ca8), 'chickpea_desi' (UWA desi v3.0, Ca1-Ca8) or 'lentil' (Chr1-Chr7). Chromosome numbe…

• legume_family

  Members of an LIS legume gene family across chickpea, lentil, pea, soybean and Medicago truncatula. gene: a chickpea/lentil/pea/Medicago gene ID, a soybean Ensembl ID (GLYMA_01G000600) or LIS name (Glyma.01G000600), or a family ID (Legume.fam3.00142). Use it to go from a soybean…

• legume_qtl

  QTL and GWAS results for legumes from the Legume Information System: soybean (SoyBase QTL on genetic maps plus GWAS; marker positions on Wm82.a2 = Ensembl glycine_max), common bean (G19833 v1 = Ensembl phaseolus_vulgaris; some GWAS on G19833 v2), cowpea (IT97K-499-35 v1) and pea…

• legume_qtl_traits

  Traits with QTL or GWAS results in the Legume Information System, with counts per species (soybean (SoyBase QTL on genetic maps plus GWAS; marker positions on Wm82.a2 = Ensembl glycine_max), common bean (G19833 v1 = Ensembl phaseolus_vulgaris; some GWAS on G19833 v2), cowpea (IT…

• lupin_markers

  Narrow-leafed lupin (Lupinus angustifolius) genetic map: 9,972 markers (DArTseq SNP/PAV, Fluidigm SNP, indel, SSR, gene-based) and domestication loci (Tardus and Lentus pod shattering, Leucospermus white flower/seed, Iucundus low alkaloid, Mollis soft seed, Ku vernalisation inde…

• expression_experiments

  Soybean and Medicago RNA-seq experiments held by askPulse (Expression Atlas and, for chickpea and pea, the Legume Information System): baseline (TPM by tissue / developmental stage / treatment) and differential (stress, pathogen, genotype contrasts). query filters descriptions/l…

• gene_expression

  Where and when a pulse and legume gene is expressed, and under which treatments it changes, from Expression Atlas and, for chickpea and pea, the Legume Information System. gene: Ensembl gene ID (e.g. GLYMA_01G000600, pea Psat1g000360), a chickpea CDC Frontier v3 ID (Ca1g000100)…

• 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…

• 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.

• 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 (pea, faba bean, Medicago, soybean, common bean, lupin) from Ensembl Compara. For each target genome, the collinear block holding most orthologues of the neighbourhood i…

• 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 a legume crop or genus name). Each paper says whether it matched an ID or a name. Name matches can be another gene with the same…

• 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 (['pisum_sativum', 'vicia_faba', 'medicago_truncatula', 'glycine_max', 'p…

• 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: pea, narrow-leafed lupin, faba bean, soybean, common bean, chickpea and lentil genomes, CDS and proteins. The program is chosen from the query and database types (blastn, o…

• pulse_gene_view

  Interactive gene view for one pulse and legume gene: a relationship map of its orthologues across legumes (Ensembl Compara), members of its LIS legume gene family (chickpea, lentil, pea, soybean, Medicago), Arabidopsis function, expression contrasts and recent papers, with tabs…

Details

More search and web servers See all

• Arcangel Trademark Search

  Free trademark availability check: is a brand name taken? USPTO search with conflict risk.

• Travel

  Flights and hotels booked in one checkout; tours, events and dining to plan; group trips.

• HeyCAi Clinic Tools

  Front-desk revenue loss calculator and website AI-search check for health clinics, by HeyCAi

• Preferly

  Free AI visibility checks for any website: AI crawler access, llms.txt, schema, business info.

• Tineo

  Plan trips, search flights and hotels, and keep every booking in one shared itinerary.

• Cellarion Wine Registry

  Public wine registry and guides: search wines, grapes, regions, appellations. No account.