PopGeV

PopGeV enables population genomic analysis by compressing and locally storing SNP and INDEL datasets and providing comparative region detection and population diversity calculations.

Key Features:

• Efficient Data Handling: Employs a novel encoding method for compressing Single Nucleotide Polymorphisms (SNPs) and Insertion-Deletion (INDEL) data to reduce storage requirements.
• IndexedDB-based Local Storage: Leverages IndexedDB technology to create local databases for retrieval of genomic data in web environments.
• Comparative Genomic Analysis: Identifies similar genomic regions between two individuals using SNP data and calculates population diversity indexes for population comparisons.
• User-Defined Annotation Integration: Supports the integration of user-defined annotation information for linking variant data to gene function.
• Scalability and Performance: Simulation results demonstrate the ability to display analysis outcomes for datasets of over 500 individuals with up to 2 million SNP data points.

Scientific Applications:

• Population Genetics: Analysis of allele frequency patterns and population diversity using SNP and INDEL datasets.
• Evolutionary Biology: Comparative detection of shared genomic regions and diversity measures to study evolutionary dynamics.
• Functional Genomics: Integration of annotation data to relate variants to gene functions.
• Variant Discovery for Traits: Identification and comparison of genetic variants associated with traits across individuals or populations.
• Comparative Population and Species Studies: Pairwise individual comparisons and population diversity calculations for cross-population or cross-species analyses.
• Annotation and Interpretation: Use of imported annotations to support interpretation of genomic variation in genes and regions of interest.

Methodology:

Uses a novel encoding method to compress SNP and INDEL data; leverages IndexedDB to create local databases and enable local data retrieval; provides functions to detect similar genomic regions between individuals using SNP data and to calculate population diversity indexes; supports integration of user-defined annotation information; performance evaluated by simulation on datasets of over 500 individuals and up to 2 million SNP data points.