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Found 57 Skills
Ingest, QC, and map reads with reproducible outputs. Use for raw read processing and coverage stats.
Build marker gene alignments and phylogenetic trees.
Cross-species gene and sequence comparison, ortholog analysis, and evolutionary conservation assessment using ToolUniverse tools. Use when comparing genes across species, finding orthologs, analyzing evolutionary conservation, or performing comparative functional annotation.
Systematic ACMG/AMP variant classification using ToolUniverse tools. Given a genetic variant (HGVS, rsID, or gene+change), applies all 28 ACMG criteria (PVS1, PS1-4, PM1-6, PP1-5, BA1, BS1-4, BP1-7) through automated database queries and computational predictions. Produces a final 5-tier classification (Pathogenic / Likely Pathogenic / VUS / Likely Benign / Benign) with evidence summary. Use when asked to classify a variant, interpret a VUS, apply ACMG criteria, assess pathogenicity, or determine clinical significance of a germline variant.
Integrate structural biology data with proteomics for drug target validation. Retrieves protein structures from PDB (RCSB, PDBe), AlphaFold predictions, antibody structures (SAbDab), GPCR data (GPCRdb), binding pocket analysis (ProteinsPlus), and ligand interactions (BindingDB). Use when asked to find structures for a drug target, identify binding site ligands, cross-validate drug binding with structural data, assess structural druggability, or compare experimental vs predicted structures.
Connect GWAS variants to biological pathways for drug target discovery. Maps disease-associated SNPs to causal genes via eQTL colocalization (GTEx), links genes to enriched pathways (Reactome, KEGG, MetaCyc), and identifies druggable targets within disease-relevant pathways. Use when asked to translate GWAS findings into mechanistic insights, find pathways enriched for disease genes, discover drug targets from genetic evidence, or answer questions like "What pathways are disrupted in type 2 diabetes based on GWAS data?"
Immunology research workflows using ToolUniverse tools. Covers antibody-antigen structural analysis (SAbDab, TheraSAbDab), immune protein interactions (IntAct, BioGRID), epitope and T-cell/B-cell assay data (IEDB), immunoglobulin gene databases (IMGT), cytokine/receptor signaling (OpenTargets, GWAS), clinical safety data for immune diseases (FAERS, clinical trials), autoimmune disease genetics (Orphanet), and immune pathway analysis (KEGG, Reactome). Use when researchers ask about antibody targets, immune signaling networks, autoimmune genetics, immunotherapy safety, epitope discovery, or immune pathway enrichment.
Analyze non-coding RNAs (miRNAs, lncRNAs, circRNAs) using miRBase, LNCipedia, RNAcentral, Rfam, and target prediction databases. Covers ncRNA identification, target prediction, disease associations, expression profiling, and functional annotation. Use when asked about microRNAs, long non-coding RNAs, RNA interference, miRNA targets, lncRNA function, or ncRNA-disease associations.
Research aging biology, cellular senescence, and longevity using ToolUniverse. Covers senescence markers and pathways, age-related disease genetics, telomere biology, senolytic drug discovery, epigenetic aging clocks, and longevity gene analysis. Integrates GWAS data, gene expression (GTEx age effects), pathway databases, drug repurposing, and literature. Use when asked about aging mechanisms, senescence, senolytics, longevity genes, age-related diseases, or epigenetic clocks.