Computational Genomics

// Computational Genomics Framework class ComputationalGenomics { constructor() { this.genomes = []; this.genes = []; this.proteins = []; this.analyses = []; } // Genome Sequencing sequenceGenome(sample, technology) { const sequencing = { sample: sample, technology: technology, reads: null, assembly: null, annotation: null, analysis: null }; // Read Generation sequencing.reads = this.generateReads(sample, technology); // Genome Assembly sequencing.assembly = this.assembleGenome(sequencing.reads); // Gene Annotation sequencing.annotation = this.annotateGenes(sequencing.assembly); // Functional Analysis sequencing.analysis = this.analyzeFunction(sequencing.annotation); return sequencing; } // Gene Expression Analysis analyzeExpression(data, conditions) { const expression = { data: data, conditions: conditions, preprocessing: null, normalization: null, differential: null, functional: null }; // Data Preprocessing expression.preprocessing = this.preprocessData(data, conditions); // Normalization expression.normalization = this.normalizeData(expression.preprocessing); // Differential Expression expression.differential = this.findDifferential(expression.normalization); // Functional Analysis expression.functional = this.analyzeFunction(expression.differential); return expression; } // Comparative Genomics compareGenomes(genomes, features) { const comparison = { genomes: genomes, features: features, alignment: null, similarity: null, divergence: null, evolution: null }; // Genome Alignment comparison.alignment = this.alignGenomes(genomes, features); // Similarity Analysis comparison.similarity = this.analyzeSimilarity(comparison.alignment); // Divergence Analysis comparison.divergence = this.analyzeDivergence(comparison.similarity); // Evolutionary Analysis comparison.evolution = this.analyzeEvolution(comparison.divergence); return comparison; } // Evolutionary Genomics analyzeEvolution(genomes, phylogeny) { const evolution = { genomes: genomes, phylogeny: phylogeny, tree: null, rates: null, selection: null, adaptation: null }; // Phylogenetic Tree evolution.tree = this.buildTree(genomes, phylogeny); // Evolutionary Rates evolution.rates = this.calculateRates(evolution.tree); // Selection Analysis evolution.selection = this.analyzeSelection(evolution.rates); // Adaptation Analysis evolution.adaptation = this.analyzeAdaptation(evolution.selection); return evolution; } // Functional Genomics analyzeFunction(genes, data) { const functional = { genes: genes, data: data, annotation: null, pathways: null, networks: null, regulation: null }; // Gene Annotation functional.annotation = this.annotateGenes(genes, data); // Pathway Analysis functional.pathways = this.analyzePathways(functional.annotation); // Network Analysis functional.networks = this.analyzeNetworks(functional.pathways); // Regulatory Analysis functional.regulation = this.analyzeRegulation(functional.networks); return functional; } // Personalized Medicine personalizeMedicine(genome, phenotype) { const personalized = { genome: genome, phenotype: phenotype, variants: null, risk: null, treatment: null, monitoring: null }; // Variant Analysis personalized.variants = this.analyzeVariants(genome, phenotype); // Risk Assessment personalized.risk = this.assessRisk(personalized.variants); // Treatment Selection personalized.treatment = this.selectTreatment(personalized.risk); // Monitoring Plan personalized.monitoring = this.planMonitoring(personalized.treatment); return personalized; } }