MySeq

MySeq performs privacy-preserving interactive analysis of personal genomes from compressed and Tabix-indexed Variant Call Format (VCF) files directly in the web browser.

Key Features:

• Browser-based execution: Performs analyses within the web browser so computations run locally rather than on remote servers.
• Privacy protection: Executes all computations locally to avoid uploading sensitive personal genomic data to external servers.
• Efficient data handling: Uses Tabix-indexing to query compressed VCF files stored locally or accessible via HTTP(s) without loading entire files into memory.
• Comprehensive analysis capabilities: Provides variant querying and annotation, physical trait prediction (e.g., bitter tasting phenotype), pharmacogenomic analysis, polygenic disease risk assessment, and ancestry analysis from VCF data.
• Extensibility: Supports extension with additional analysis or visualization components.

Scientific Applications:

• Education: Enables hands-on genome exploration and analysis for classroom and instructional use.
• Personalized genomics research: Supports variant-level analysis, trait prediction, pharmacogenomic interpretation, polygenic risk assessment, and ancestry investigations in personalized genomics studies.

Methodology:

Developed using React.js and executed entirely in the web browser; leverages Tabix-indexing to query compressed-and-indexed VCF files stored locally or reachable via HTTP(s) without loading whole files into memory, and performs analyses locally to prevent external data transfer.