FractBias

FractBias assesses fractionation bias following polyploidy by identifying syntenic regions and quantifying gene retention and loss across homeologous chromosomes to characterize non-random patterns of genomic fractionation.

Key Features:

• Gene Retention and Fractionation Analysis: Calculates and visualizes gene retention and fractionation patterns across whole genomes by identifying and analyzing syntenic regions.
• Synteny Identification: Identifies syntenic regions as blocks of conserved genes across species to map homeologous chromosomes and retained or lost genes.
• Integration with SynMap/CoGe: Integrates with SynMap, a component of the Comparative Genomics Platform (CoGe), to utilize pre-loaded assembled genomes for analysis.

Scientific Applications:

• Evolutionary Genomics: Analyzes selective pressures and evolutionary mechanisms that influence gene retention following polyploidy.
• Genome Evolution and Adaptation: Provides insights into species adaptation and genome evolution through patterns of retained versus lost genes.
• Functional Genomics: Informs the functional implications of genes retained or lost after polyploidy events.

Methodology:

Identifies syntenic regions (blocks of conserved genes), analyzes syntenic datasets to calculate gene retention and fractionation patterns, and generates plots of gene retention; integrates with SynMap/CoGe for pre-loaded assembled genomes.