Plant Genomics

Fetch the AlphaFold DB predicted-structure summary for a locus (alphafold.ebi.ac.uk; free, no key). Resolves the locus → UniProt accession, then returns the predicted model's global mean pLDDT confidence, the per-band pLDDT distribution with each band's pLDDT range (plddt_band_ranges), modelled residue span, latest model version, and mmCIF / PDB / PAE download URLs — links for the client to fetch; no tool on this server retrieves them. A valid protein with no deposited model returns found=false (a normal outcome, not an error); a locus with no UniProt entry raises a typed NotFoundError. Works for all 12 organisms (UniProt-keyed). Complements resolve_locus_to_uniprot (sequence-level) with the structure-level view. Defaults to arabidopsis_thaliana; pass organism= for other species.

Synthesis: one-call equivalent of the analyze_locus prompt. Resolves a locus through Ensembl Plants, then fans out to xrefs, UniProt, Europe PMC, and QuickGO in parallel. Returns a SynthesisEnvelope with per-step status and a reconciled summary flagging cross-source name/accession disagreements.

Fetch 1001 Genomes natural-variation SNP effects for an Arabidopsis locus (tools.1001genomes.org; free, no key) — the variation observed across 1135 resequenced natural accessions. Returns per-SNP effect rows (chromosome, position, accession id, effect, impact, amino-acid change, transcript) plus the gene's genomic span. variant_count is the true row total even when capped. ARABIDOPSIS-ONLY — any other organism raises OrganismNotSupported. Defaults to arabidopsis_thaliana.

Fetch AraGWAS genome-wide association study hits for an Arabidopsis locus (aragwas.1001genomes.org; free, no key). Returns each significant SNP association overlapping the gene with its score (-log10 p), minor-allele frequency, the SNP's predicted molecular effect (impact, amino-acid change), and the phenotype/study it came from, including the study's own significance thresholds on the score's scale (study.thresholds), which the over_bonferroni / over_fdr / over_permutation flags are taken against. Rows come strongest first, 25 per answer by default (limit, up to 100); next_cursor resumes at the first row not returned. association_count is the true total even when page-capped. ARABIDOPSIS-ONLY — any other organism raises OrganismNotSupported. Defaults to arabidopsis_thaliana.

Fetch co-expressed gene neighbors from ATTED-II (atted.jp, API v5) for a plant locus. Returns top_n neighbors with target locus + NCBI Entrez gene ID + score (higher = stronger coexpression), in the index the release declares as score_type: 'z' for Ath-u.c4-0, 'LSmr' (logit score) for the other releases. The ATTED-II release (e.g. Ath-u.c4-0 for Arabidopsis, Osa-u.c1-0 for rice) is resolved per-organism. Covers: arabidopsis_thaliana, glycine_max, medicago_truncatula, oryza_sativa, solanum_lycopersicum, vitis_vinifera, zea_mays. Any other organism raises OrganismNotSupported before any request (both the single and batch forms). A locus that is not in the organism's release raises NotFoundError. Pairs with string_interactions to surface high-confidence functional partners (interactors that are also coexpressed).

Fetch BAR AIV (Arabidopsis Interactions Viewer) interactions for an Arabidopsis or rice locus. Dispatches by organism: Arabidopsis returns curated GRN paper refs from /interactions/get_paper_by_agi/{locus} (PubMed ID, title, image URL, comments, pipe-split tags; the image is a link for the client to fetch, no tool on this server retrieves it); rice returns predicted PPI partners from /interactions/rice/{locus} with Pearson co-expression r (pcc), evidence hits, and quality score. The `kind` field discriminates the response shape (grn_papers vs ppi_predictions). Rice requires the MSU LOC_Os* locus format — RAP-DB Os*g* is rejected upstream. Only Arabidopsis and rice are supported by AIV; other organisms raise OrganismNotSupported.

Fetch BAR/eFP world-map natural-variation expression for an Arabidopsis locus. Wraps the world-eFP view at /microarray_gene_expression/world_efp/arabidopsis/{locus} — returns expression across ~36 ecotypes (Bay-0, Col-0, Cvi-1, Ler-2, ...) with per-replicate values, control samples, collection lat/lng, and a per-ecotype mean computed client-side. Arabidopsis only. BAR is keyless and a Global Core Biodata Resource (2023).

Fetch the BAR (Bio-Analytic Resource, U Toronto) merged ThaleMine + GAIA-aliases summary for an Arabidopsis locus. Returns the TAIR curator summary + Araport11 computational description from /thalemine/gene_information/ together with the NCBI Gene ID and cross-DB aliases (RefSeq, UniProt, TIGR locus-model IDs) from /gaia/aliases/. Arabidopsis only — ThaleMine carries taxon 3702 plus yeast/human for ortholog cross-reference. BAR is keyless and a Global Core Biodata Resource (2023); replaces the v0.9 subscription-gated tair_locus_info stub for the curator-summary use case.

Batch version of atted_coexpression. Up to 50 loci per call. Covers: arabidopsis_thaliana, glycine_max, medicago_truncatula, oryza_sativa, solanum_lycopersicum, vitis_vinifera, zea_mays. Any other organism raises OrganismNotSupported before any request (both the single and batch forms).

Batch variant of bar_aiv_interactions. Fans out per-locus BAR AIV calls in parallel (up to 50 loci); all loci in a single call share the same organism. Each results[locus] is the full single-locus payload (kind=grn_papers for Arabidopsis with `papers` list, kind=ppi_predictions for rice with `partners` list).

Batch variant of bar_gene_summary. Fans out per-locus BAR ThaleMine + GAIA-aliases calls in parallel (up to 50 loci). Each results[locus] is the full single-locus payload (curator summary, computational description, NCBI Gene ID, cross-DB aliases). Arabidopsis only.

Batch variant of ensembl_plants_lookup_locus. Uses Ensembl's native POST /lookup/id endpoint — one HTTP round-trip for up to 50 loci, materially cheaper than N parallel GETs. Successes in results[] with the same shape as the single-locus tool. Retries 429/5xx via the shared `_http` helper (Retry-After capped at 60 s). Misses (loci with no record) still land in `errors[]` with the `[NotFoundError]` prefix; the whole batch only fails when the retry budget is exhausted.

Batch variant of get_gene_xrefs. Fans out per-locus xref lookups over Ensembl Plants in parallel (up to 50 loci). Each results[locus] is the full single-locus shape (count + xrefs[] + by_db rollup).

Batch version of gramene_homologs. Up to 50 loci per call; shares the homology_type filter across all loci. Returns the standard batch envelope (count + results dict + errors dict).

Batch version of kegg_pathways. Up to 50 loci per call. Covers: arabidopsis_thaliana, brachypodium_distachyon, glycine_max, hordeum_vulgare, oryza_sativa, populus_trichocarpa, zea_mays. Any other organism raises OrganismNotSupported before any request (both the single and batch forms).

Run one locus-keyed tool over up to 50 loci in one call (#131). 'tool' names any tool whose only required argument is 'locus' (interpro_domains, alphafold_structure, panther_family, orthodb_orthologs, gene_report, ...); 'args' holds that tool's other arguments, shared by every locus and checked against its schema once before any call. Returns the standard batch envelope: results keyed by locus, each exactly what the single tool returns, and per-locus errors. The dedicated batch_* tools remain.

Batch variant of locus_go_annotations. Two-stage fanout — each locus is resolved to UniProt and then queried in QuickGO. Per-locus NotFoundError from either stage lands in errors[] with the typed prefix preserved. Capped at 50 loci.

Batch variant of locus_literature. Fans out per-locus Europe PMC searches in parallel (up to 50 loci). Each results[locus] is the full single-locus payload (query + hitCount + returned + hits[]).

Batch variant of phytozome_lookup_locus. Fans out per-locus BioMart queries in parallel (up to 50 loci). Each results[locus] is the full single-locus row (organism_name, gene_name, chromosome, start/end/strand, description).

Batch variant of resolve_locus_to_uniprot. Fans out per-locus UniProtKB searches in parallel (up to 50 loci). Each results[locus] is the full single-locus record (primaryAccession + uniProtkbId + entryType + geneNames + organism + sequenceLength + web_url + …).

Batch version of string_interactions. Up to 50 inputs per call. The argument was called loci_or_accessions before #129; that name is still accepted, deprecated.

Synthesis: one-call equivalent of the biological_context prompt. Resolves UniProt accession, then fans out to Gramene homologs, KEGG pathways, STRING-DB partners, and ATTED-II coexpression in parallel. Adds a consensus_partners ranking that merges STRING + ATTED scores.

Run a BLAST sequence-similarity search against NCBI BLAST URLAPI. Async Put/Get under the hood — submits the query, polls the RID (honoring NCBI's per-RID 60s floor), and returns the parsed top hits + raw text report excerpt. Programs: blastn / blastp / blastx / tblastn / tblastx. Database defaults to swissprot for protein programs, core_nt for nucleotide. Emits notifications/progress on each poll. Long searches (>10 min) raise [UpstreamUnavailableError] with the RID preserved so the client can re-poll. Set PLANT_GENOMICS_MCP_NCBI_EMAIL to identify the request per NCBI etiquette.

Synthesis: cross-source homology consensus. Resolves UniProt + FASTA sequence, then runs Gramene homology calls and NCBI BLAST in parallel. Dedupes hits by normalized locus token and scores by n_sources * mean_identity — Gramene contributes identity=1.0, BLAST contributes pident/100.

Describe an organism's Ensembl assembly (rest.ensembl.org /info/assembly; free, no key): assembly name, GCA accession and date, the karyotype, and every top-level seq-region with its length. The names are the region values ensembl_region_query takes, and a start past a region's length is refused there, so a region walk can be planned before the first call. Karyotype regions come first, in karyotype order, then unplaced scaffolds and contigs, longest first. Names are Ensembl's: tomato's chromosomes are CM001064.4 and so on, not '1'. coord_system labels differ between assemblies (chromosome, scaffold, supercontig, primary_assembly), so in_karyotype, not coord_system, says which regions are chromosomes. total counts every region before limit; truncated=true when limit cut some off (soybean has over 1,100).

Fetch metadata for a plant locus identifier from Ensembl Plants. Defaults to arabidopsis_thaliana; pass organism= for other plant species (oryza_sativa, zea_mays, ...). Locus is the TAIR-style identifier (e.g. AT1G01010 for Arabidopsis NAC001).

List the paralogues Ensembl Compara (plants) records for a plant locus (rest.ensembl.org /homology, type=paralogues; free, no key). Each row gives the paralogue's locus, its type — within_species_paralog, or other_paralog: Ensembl's 'ancient paralogues', inferred across a super tree, so the two genes can sit in different gene trees — the taxonomy_level of the duplication, perc_id/perc_pos and protein_id, closest first. gramene_homologs carries only within_species_paralog, so a gene can have paralogues here and none there. A paralogue list is not a family list: other_paralog can name a gene outside the family (AT2G23390, an acyl-CoA N-acyltransferase-like gene, is an other_paralog of the ARFs); test membership with interpro_domains. An empty list means Compara records no paralogue, not that the gene is single-copy (FLS2, AT5G46330, has none). found=false when Compara keeps no homology record for the gene at all (e.g. a non-coding gene); an id Ensembl does not know is a not-found error. total and counts_by_type count before limit; truncated=true when limit cut some off.

List features overlapping a genomic interval via Ensembl Plants /overlap/region. region is the seq-region name (chromosome / contig, e.g. '1'); start and end are 1-based inclusive. feature is one of gene / transcript / cds / exon (default gene). Answers 'what genes are in this QTL interval / assembly window' without a per-locus lookup. Ensembl caps the span — oversized regions error. ensembl_plants_assembly lists an organism's region names and their lengths; a region outside that list, or a start past its length, is an error here. Defaults to arabidopsis_thaliana; pass organism= for other species.

List every protein in one organism that carries an InterPro, Pfam or PANTHER entry, with the gene locus each maps to — the reverse of interpro_domains / panther_family (entry -> genes, not gene -> entries). One UniProt query (rest.uniprot.org; free, no key). Each member gives accession, symbol and locus; locus is the id the locus-keyed tools accept, or null when UniProt links the protein to no gene (e.g. an old cDNA submission). reviewed_only=true (default) keeps Swiss-Prot entries: complete for Arabidopsis and rice, empty for most other crops, so pass reviewed_only=false there. total is UniProt's count across all pages; when truncated=true, pass next_cursor back as cursor= for the next page. An entry absent from the organism is ok with total 0. Defaults to arabidopsis_thaliana.

Fetch CURATED EXPERIMENTAL protein/genetic interaction partners for an Arabidopsis locus from ThaleMine (BAR's InterMine instance; free, no key), sourced from BioGRID, IntAct and PSI-MI. Unlike string_interactions (predicted / text-mined, scored) and bar_aiv_interactions (which returns GRN *paper references* for Arabidopsis, not partner pairs), every partner here carries the actual experimental provenance: detection method (two hybrid, pull down, genetic interference, ...), PSI-MI relationship type, physical vs genetic class, source database, and the PubMed IDs that reported it. ThaleMine emits one row per evidence record, so rows are aggregated to one entry per partner with evidence_count as a crude support signal; partners are ordered by that count. found=false means the gene is real but has no curated interaction on record — a normal outcome; an unknown locus raises a typed NotFoundError. Arabidopsis only (ThaleMine carries genes for taxon 3702; other organisms raise OrganismNotSupported).

Fetch experimentally-solved (X-ray / cryo-EM / NMR) protein structures for a locus from PDBe (www.ebi.ac.uk/pdbe; free, no key). Resolves the locus → UniProt accession, then returns PDBe's best_structures mapping ranked best-first: per entry the PDB id, chain, experimental method, resolution, coverage, and modelled residue span. Most plant proteins have NO deposited structure — that returns found=false (a normal outcome, not an error); a locus with no UniProt entry raises a typed NotFoundError. structure_count is the true total even when the list is capped. Complements alphafold_structure (the predicted view). Works for all 12 organisms (UniProt-keyed). Defaults to arabidopsis_thaliana; pass organism= for other species.

Synthesis: one-call equivalent of the find_homologs prompt. Runs BLAST then resolves UniProt-shaped subject accessions via the batch UniProt helper. Returns ranked hits each annotated with their UniProt record (or null if subject_id is not a UniProt accession).

Synthesis: one-shot 'tell me about this gene' dossier. Resolves a locus through Ensembl Plants + UniProt, then fans out to cross-references, KEGG pathways, STRING interactors, Europe PMC literature, and QuickGO GO terms. Returns a SynthesisEnvelope whose result.markdown is a rendered Markdown gene dossier (the headline output) alongside a structured result.sections mirror; each backend payload appears once, under sections, while steps[] carries status and per-step timing only. The literature section carries no abstracts (abstracts_included: false) and the GO section no withFrom (with_from_included: false); locus_literature and locus_go_annotations return them. result.gene_names labels the Ensembl and UniProt gene names separately when they differ. Any single backend failure degrades that section to an 'Unavailable' note; the rest of the dossier still renders.

List the member genes of an Ensembl Compara (plants) gene tree (rest.ensembl.org /genetree; free, no key). Name the tree by locus= (any member gene, with organism=) and Ensembl finds the tree that gene is in now, or by gene_tree_id=; exactly one. A gramene_homologs gene_tree_id comes from an older Compara release and may not exist here, so prefer locus=. Each member gives the locus (the id the locus-keyed tools accept), protein_id, species and taxid, and organism (the canonical slug, or null for a species outside this server's 12). target_organism= keeps one organism's members; omit it for every species. total counts members before limit; truncated=true when limit cut some off. gene_tree_id in the answer is the tree served. An unknown tree id, or a locus in no tree, is a not-found error.

Fetch cross-database references (UniProt, NCBI Gene, TAIR, ArrayExpress, …) for a plant locus from Ensembl Plants. Defaults to arabidopsis_thaliana; pass organism= for other Ensembl Plants species. Returns count + raw xref list + a by_db rollup keyed on Ensembl's dbname (e.g. 'Uniprot_gn', 'EntrezGene') for fast lookup of a single foreign identifier.

Fetch a locus's sequence from Ensembl Plants. seq_type is one of genomic / cds / cdna / protein (default protein — the canonical-transcript product). Closes the lookup → fetch → BLAST loop: feed the returned `sequence` straight to blast_sequence (protein for blastp, cds/cdna for blastn). Defaults to arabidopsis_thaliana; pass organism= for other plant species.

GO + KEGG over-representation analysis for a gene LIST via g:Profiler g:GOSt (biit.cs.ut.ee/gprofiler; free, no API key). Unlike locus_go_annotations (one locus → its terms), this answers 'what is my gene SET enriched for?' — the dominant question for a differential-expression or co-expression cluster. loci is the query gene list (e.g. AT-codes for Arabidopsis, RAP-DB IDs for rice). sources defaults to GO:BP/GO:MF/GO:CC + KEGG; user_threshold is the g:SCS-corrected significance cutoff (default 0.05). Optional background sets a custom statistical domain (default: all annotated genes). Returns enriched[] (term_id/name/p_value/intersection_size/…, capped at top_n by p-value) plus unmapped[] — query loci g:Profiler could not recognize, surfaced so a locus-namespace mismatch is visible. Defaults to arabidopsis_thaliana; pass organism= for any of the 12 species.

Fetch orthologs and paralogs for a plant locus from Gramene compara (data.gramene.org v69). Default homology_type='ortholog'; pass 'paralog' for in-species duplicates or 'all' for everything. 'ortholog' includes syntenic_ortholog_* rows; homoeologs (polyploid subgenome copies) come back only under 'all', and excluded_categories counts every category the filter left out. Returns target_locus + homology category (type) + shared gene_tree_id per hit (Gramene's tree id; for the tree's members pass the locus to gene_tree_members). Rows carry no taxon unless with_organism=true (adds 'organism' per row) or target_organism is given, which filters to one organism before the cap and adds 'organism' per row. Paralogs here are within_species_paralog only: Gramene drops Compara's other_paralog ('ancient paralogues'); ensembl_plants_paralogs lists both. Pair with resolve_locus_to_uniprot for protein-level enrichment and with blast_sequence for sequence similarity discovery.