{ "server": "gget", "toolCount": 19, "tools": [ { "name": "gget_search", "description": "Search for genes using gene symbols, names, or synonyms.\n \n Use this tool FIRST when you have gene names/symbols and need to find their Ensembl IDs.\n Returns Ensembl IDs which are required for get_gene_info and get_sequences tools.\n \n Args:\n search_terms: List of gene symbols (e.g., ['TP53', 'BRCA1']) or names\n species: Target species (e.g., 'homo_sapiens', 'mus_musculus')\n limit: Maximum number of results per search term\n \n Example:\n Input: search_terms=['BRCA1'], species='homo_sapiens'\n Output: {'BRCA1': {'ensembl_id': 'ENSG00000012048', 'description': 'BRCA1 DNA repair...'}}\n \n Downstream tools that need the Ensembl IDs from this search:\n - get_gene_info: Get detailed gene information \n - get_sequences: Get DNA/protein sequences\n ", "inputSchema": { "type": "object", "properties": { "search_terms": { "items": { "type": "string" }, "title": "Search Terms", "type": "array" }, "species": { "default": "homo_sapiens", "title": "Species", "type": "string" }, "limit": { "default": 100, "title": "Limit", "type": "integer" } }, "required": [ "search_terms" ] } }, { "name": "gget_info", "description": "Get detailed information for genes using their Ensembl IDs.\n \n PREREQUISITE: Use search_genes first to get Ensembl IDs from gene names/symbols.\n \n Args:\n ensembl_ids: List of Ensembl gene IDs (e.g., ['ENSG00000141510'])\n verbose: Include additional annotation details\n \n Example workflow:\n 1. search_genes(['TP53'], 'homo_sapiens') → get Ensembl ID 'ENSG00000141510'\n 2. get_gene_info(['ENSG00000141510']) \n \n Example output:\n {'ENSG00000141510': {'symbol': 'TP53', 'biotype': 'protein_coding', \n 'start': 7661779, 'end': 7687550, 'chromosome': '17'...}}\n ", "inputSchema": { "type": "object", "properties": { "ensembl_ids": { "items": { "type": "string" }, "title": "Ensembl Ids", "type": "array" }, "verbose": { "default": true, "title": "Verbose", "type": "boolean" } }, "required": [ "ensembl_ids" ] } }, { "name": "gget_seq", "description": "Fetch nucleotide or amino acid sequences for genes.\n \n PREREQUISITE: Use search_genes first to get Ensembl IDs from gene names/symbols.\n \n Args:\n ensembl_ids: List of Ensembl gene IDs (e.g., ['ENSG00000141510'])\n translate: If True, returns protein sequences; if False, returns DNA sequences\n isoforms: Include alternative splice isoforms\n \n Example workflow for protein sequence:\n 1. search_genes(['TP53'], 'homo_sapiens') → 'ENSG00000141510'\n 2. get_sequences(['ENSG00000141510'], translate=True)\n \n Example output (protein):\n {'ENSG00000141510': 'MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSP...'}\n \n Example output (DNA):\n {'ENSG00000141510': 'ATGGAGGAGCCGCAGTCAGATCCTAGCGTCGAGCCCCCTCTGAGTC...'}\n \n Downstream tools that use protein sequences:\n - alphafold_predict: Predict 3D structure from protein sequence\n - blast_sequence: Search for similar sequences\n ", "inputSchema": { "type": "object", "properties": { "ensembl_ids": { "items": { "type": "string" }, "title": "Ensembl Ids", "type": "array" }, "translate": { "default": false, "title": "Translate", "type": "boolean" }, "isoforms": { "default": false, "title": "Isoforms", "type": "boolean" } }, "required": [ "ensembl_ids" ] } }, { "name": "gget_ref", "description": "Get reference genome information from Ensembl.", "inputSchema": { "type": "object", "properties": { "species": { "default": "homo_sapiens", "title": "Species", "type": "string" }, "which": { "default": "all", "title": "Which", "type": "string" }, "release": { "anyOf": [ { "type": "integer" }, { "type": "null" } ], "default": null, "title": "Release" } } } }, { "name": "gget_blast", "description": "BLAST a nucleotide or amino acid sequence.", "inputSchema": { "type": "object", "properties": { "sequence": { "title": "Sequence", "type": "string" }, "program": { "default": "blastp", "title": "Program", "type": "string" }, "database": { "default": "nr", "title": "Database", "type": "string" }, "limit": { "default": 50, "title": "Limit", "type": "integer" }, "expect": { "default": 10, "title": "Expect", "type": "number" } }, "required": [ "sequence" ] } }, { "name": "gget_blat", "description": "Find genomic location of a sequence using BLAT.", "inputSchema": { "type": "object", "properties": { "sequence": { "title": "Sequence", "type": "string" }, "seqtype": { "default": "DNA", "title": "Seqtype", "type": "string" }, "assembly": { "default": "hg38", "title": "Assembly", "type": "string" } }, "required": [ "sequence" ] } }, { "name": "gget_muscle", "description": "Align multiple sequences using MUSCLE.", "inputSchema": { "type": "object", "properties": { "sequences": { "items": { "type": "string" }, "title": "Sequences", "type": "array" }, "super5": { "default": false, "title": "Super5", "type": "boolean" } }, "required": [ "sequences" ] } }, { "name": "gget_diamond", "description": "Align amino acid sequences to a reference using DIAMOND.", "inputSchema": { "type": "object", "properties": { "sequences": { "anyOf": [ { "type": "string" }, { "items": { "type": "string" }, "type": "array" } ], "title": "Sequences" }, "reference": { "title": "Reference", "type": "string" }, "sensitivity": { "default": "very-sensitive", "title": "Sensitivity", "type": "string" }, "threads": { "default": 1, "title": "Threads", "type": "integer" } }, "required": [ "sequences", "reference" ] } }, { "name": "gget_archs4", "description": "Get tissue expression data from ARCHS4.", "inputSchema": { "type": "object", "properties": { "gene": { "title": "Gene", "type": "string" }, "which": { "default": "tissue", "title": "Which", "type": "string" }, "species": { "default": "human", "title": "Species", "type": "string" } }, "required": [ "gene" ] } }, { "name": "gget_enrichr", "description": "Perform functional enrichment analysis using Enrichr.", "inputSchema": { "type": "object", "properties": { "genes": { "items": { "type": "string" }, "title": "Genes", "type": "array" }, "database": { "default": "KEGG_2021_Human", "title": "Database", "type": "string" }, "species": { "default": "human", "title": "Species", "type": "string" } }, "required": [ "genes" ] } }, { "name": "gget_bgee", "description": "Find orthologs of a gene using Bgee database.\n \n PREREQUISITE: Use search_genes to get Ensembl ID first.\n \n Args:\n gene_id: Ensembl gene ID (e.g., 'ENSG00000012048' for BRCA1)\n type: Type of data ('orthologs' or 'expression')\n \n Example workflow:\n 1. search_genes(['BRCA1']) → 'ENSG00000012048' \n 2. bgee_orthologs('ENSG00000012048') → ortholog data\n ", "inputSchema": { "type": "object", "properties": { "gene_id": { "title": "Gene Id", "type": "string" }, "type": { "default": "orthologs", "title": "Type", "type": "string" } }, "required": [ "gene_id" ] } }, { "name": "gget_pdb", "description": "Fetch protein structure data from PDB using specific PDB IDs.\n \n IMPORTANT: This tool requires a specific PDB ID (e.g., '2GS6'), NOT gene names.\n \n For gene-to-structure workflows:\n 1. Use search_genes to get Ensembl ID\n 2. Use get_sequences with translate=True to get protein sequence \n 3. Use alphafold_predict for structure prediction, OR\n 4. Search external databases (PDB website) for known PDB IDs, then use this tool\n \n Args:\n pdb_id: Specific PDB structure ID (e.g., '2GS6', '1EGF')\n resource: Database resource ('pdb' or 'alphafold')\n \n Example:\n Input: pdb_id='2GS6'\n Output: Structure data with coordinates, resolution, method, etc.\n \n Alternative workflow for gene structure prediction:\n 1. search_genes(['EGFR']) → get Ensembl ID\n 2. get_sequences([ensembl_id], translate=True) → get protein sequence\n 3. alphafold_predict(protein_sequence) → predict structure\n ", "inputSchema": { "type": "object", "properties": { "pdb_id": { "title": "Pdb Id", "type": "string" }, "resource": { "default": "pdb", "title": "Resource", "type": "string" } }, "required": [ "pdb_id" ] } }, { "name": "gget_alphafold", "description": "Predict protein structure using AlphaFold from protein sequence.\n \n PREREQUISITE: Use get_sequences with translate=True to get protein sequence first.\n \n Workflow for gene structure prediction:\n 1. search_genes → get Ensembl ID\n 2. get_sequences with translate=True → get protein sequence\n 3. alphafold_predict → predict structure\n \n Args:\n sequence: Amino acid sequence (protein, not DNA)\n out: Optional output directory for structure files\n \n Example full workflow:\n 1. search_genes(['TP53']) → 'ENSG00000141510'\n 2. get_sequences(['ENSG00000141510'], translate=True) → 'MEEPQSDPSVEPPLSQ...'\n 3. alphafold_predict('MEEPQSDPSVEPPLSQ...')\n \n Example output:\n AlphaFold structure prediction data with confidence scores and coordinates\n ", "inputSchema": { "type": "object", "properties": { "sequence": { "title": "Sequence", "type": "string" }, "out": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Out" } }, "required": [ "sequence" ] } }, { "name": "gget_elm", "description": "Find protein interaction domains and functions in amino acid sequences.", "inputSchema": { "type": "object", "properties": { "sequence": { "title": "Sequence", "type": "string" }, "sensitivity": { "default": "very-sensitive", "title": "Sensitivity", "type": "string" }, "threads": { "default": 1, "title": "Threads", "type": "integer" }, "uniprot": { "default": false, "title": "Uniprot", "type": "boolean" }, "expand": { "default": false, "title": "Expand", "type": "boolean" } }, "required": [ "sequence" ] } }, { "name": "gget_cosmic", "description": "Search COSMIC database for cancer mutations and cancer-related data.\n \n Args:\n searchterm: Gene symbol or name to search for (e.g., 'PIK3CA', 'BRCA1')\n cosmic_tsv_path: Path to COSMIC TSV file (optional, uses default if None)\n limit: Maximum number of results to return\n \n Example:\n Input: searchterm='PIK3CA'\n Output: Mutation data including positions, amino acid changes, cancer types, etc.\n \n Note: This tool accepts gene symbols directly, no need for Ensembl ID conversion.\n ", "inputSchema": { "type": "object", "properties": { "searchterm": { "title": "Searchterm", "type": "string" }, "cosmic_tsv_path": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Cosmic Tsv Path" }, "limit": { "default": 100, "title": "Limit", "type": "integer" } }, "required": [ "searchterm" ] } }, { "name": "gget_mutate", "description": "Mutate nucleotide sequences based on specified mutations.", "inputSchema": { "type": "object", "properties": { "sequences": { "anyOf": [ { "type": "string" }, { "items": { "type": "string" }, "type": "array" } ], "title": "Sequences" }, "mutations": { "anyOf": [ { "type": "string" }, { "items": { "type": "string" }, "type": "array" } ], "title": "Mutations" }, "k": { "default": 30, "title": "K", "type": "integer" } }, "required": [ "sequences", "mutations" ] } }, { "name": "gget_opentargets", "description": "Explore diseases and drugs associated with a gene using Open Targets.\n \n PREREQUISITE: Use search_genes to get Ensembl ID first.\n \n Args:\n ensembl_id: Ensembl gene ID (e.g., 'ENSG00000141510' for APOE)\n resource: Type of information ('diseases', 'drugs', 'tractability', etc.)\n limit: Maximum number of results (optional)\n \n Example workflow:\n 1. search_genes(['APOE']) → 'ENSG00000141510'\n 2. opentargets_analysis('ENSG00000141510') → disease associations\n ", "inputSchema": { "type": "object", "properties": { "ensembl_id": { "title": "Ensembl Id", "type": "string" }, "resource": { "default": "diseases", "title": "Resource", "type": "string" }, "limit": { "anyOf": [ { "type": "integer" }, { "type": "null" } ], "default": null, "title": "Limit" } }, "required": [ "ensembl_id" ] } }, { "name": "gget_cellxgene", "description": "Query single-cell RNA-seq data from CellxGene.", "inputSchema": { "type": "object", "properties": { "gene": { "anyOf": [ { "items": { "type": "string" }, "type": "array" }, { "type": "null" } ], "default": null, "title": "Gene" }, "tissue": { "anyOf": [ { "items": { "type": "string" }, "type": "array" }, { "type": "null" } ], "default": null, "title": "Tissue" }, "cell_type": { "anyOf": [ { "items": { "type": "string" }, "type": "array" }, { "type": "null" } ], "default": null, "title": "Cell Type" }, "species": { "default": "homo_sapiens", "title": "Species", "type": "string" } } } }, { "name": "gget_setup", "description": "Setup databases for gget modules that require local data.", "inputSchema": { "type": "object", "properties": { "module": { "title": "Module", "type": "string" } }, "required": [ "module" ] } } ], "fetchedAt": "2025-06-07T16:03:53.518Z" }