PGAP

PGAP performs comprehensive pan-genome analysis of prokaryotic genomes to identify core, accessory, and unique gene sets and to analyze gene clusters, functional gene variation, functional enrichment, and species evolution.

Key Features:

• Cluster Analysis of Functional Genes: Enables clustering and categorization of functional genes across strains or species.
• Pan-Genome Profile Analysis: Constructs pan-genome profiles to define core, accessory, and unique gene sets across genomes.
• Genetic Variation Analysis of Functional Genes: Detects and characterizes mutations and polymorphisms within functional genes.
• Species Evolution Analysis: Infers phylogenetic relationships and evolutionary trajectories among species from genomic data.
• Function Enrichment Analysis of Gene Clusters: Identifies overrepresented biological functions within gene clusters through enrichment analysis.

Scientific Applications:

• Bacterial Genomics: Applied to comparative analyses of bacterial genomes to study genetic diversity and evolutionary patterns.
• Streptococcus pyogenes Case Study: Demonstrated on 11 strains of Streptococcus pyogenes for pan-genome and comparative analyses.

Methodology:

Implemented as Perl scripts on a Linux platform.