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Pulse and legume genes, LIS gene families, expression, QTL, germplasm and papers
Remote server: your requests and data go to askpulse.plantdatabases.org. Claude Code: claude mcp add --transport http askpulse https://askpulse.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 askPulse resources (genes, germplasm, genotyping datasets, files). Filters (exact values): database e.g. 'Ensembfind_germplasm — Find pulse and legume genebank accessions by accession number or name (e.g. 'ICC 4958' for chickpea at ICRISAT): chickpea, lentil, pea, fabadata_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 agenes_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', 'glycineorthologues — Orthologues of a gene from Ensembl Plants Compara (gene trees across plant genomes), e.g. the Brassica copies of an Arabidopsis gene. gene: arabidopsis_function — Function of a gene through its Arabidopsis thaliana orthologue(s): Ensembl Plants Compara orthologues, then UniProtKB curated function, protlegume_gene — Chickpea or lentil gene from the Legume Information System (these genomes are not in Ensembl Plants): location, functional description, LIS legume_pangene — The same gene across chickpea or pea assemblies and annotation versions, from LIS pangene sets (synteny-aware clustering). Chickpea (Cicer.plegume_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-clegume_family — Members of an LIS legume gene family across chickpea, lentil, pea, soybean and Medicago truncatula. gene: a chickpea/lentil/pea/Medicago genlegume_qtl — QTL and GWAS results for legumes from the Legume Information System: soybean (SoyBase QTL on genetic maps plus GWAS; marker positions on Wm8legume_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; mlupin_markers — Narrow-leafed lupin (Lupinus angustifolius) genetic map: 9,972 markers (DArTseq SNP/PAV, Fluidigm SNP, indel, SSR, gene-based) and domesticaexpression_experiments — Soybean and Medicago RNA-seq experiments held by askPulse (Expression Atlas and, for chickpea and pea, the Legume Information System): baselgene_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,expression_genes — Genes characteristic of a tissue/stage or responsive to a treatment in one Expression Atlas experiment. Baseline experiment + group (text masearch_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.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 (pea, faba bean, Medicago, soygene_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: pea, narrow-leafed lupin, faba bepulse_gene_view — Interactive gene view for one pulse and legume gene: a relationship map of its orthologues across legumes (Ensembl Compara), members of its Not tested by KitScout yet. When our harness runs it, pros, cons and the tasks we tried appear here, with the date and evidence.