PanGeneHome

PanGeneHome provides pre-computed pangenome analyses to characterize gene conservation, pangenome/core-genome dynamics, dendrograms based on gene content and average amino acid identity (AAI), and functional and metabolic pathway composition across microbial taxa.

Key Features:

• Pre-computed analyses: Pre-computed pangenome results including gene conservation metrics, pangenome/core-genome curves, dendrograms, and functional assignments.
• Extensive coverage: Coverage for 615 taxa encompassing 182 species across 49 orders.
• Conservation level of genes: Assessment of gene conservation within and across taxa.
• Pangenome and core-genome curves: Curves provided to estimate pangenome and core-genome sizes and dynamics.
• Dendrograms: Dendrograms derived from gene content and average amino acid identity (AAI) to represent genomic relationships.
• Functional categories and metabolic pathways: Assignment of core, accessory, and unique gene pools to functional categories and metabolic pathways.
• Comparative analysis: Comparative metrics and functional composition comparisons across different taxa.
• Regular updates: Database updates to incorporate newly sequenced microbial genomes and expand taxa coverage.

Scientific Applications:

• Pangenome characterization: Quantify pangenome and core-genome sizes and assess their dynamics across taxa.
• Phylogenomic inference: Infer genomic similarity and evolutionary relationships using gene-content and AAI-based dendrograms.
• Functional and pathway profiling: Compare distributions of functional categories and metabolic pathways among core, accessory, and unique gene pools.
• Comparative genomics: Enable cross-taxa comparisons of gene conservation, pangenome metrics, and functional composition.

Methodology:

Computations include assessment of gene conservation, construction of pangenome and core-genome curves, generation of dendrograms from gene content and average amino acid identity (AAI), and assignment of genes to functional categories and metabolic pathways.