panRGP

panRGP predicts Regions of Genome Plasticity (RGPs) from pangenome graphs to identify Genomic Islands (GIs) and their insertion spots across prokaryotic genomes.

Key Features:

• Pangenome-Based Methodology: panRGP constructs pangenome graphs from all available genomes of a species to detect variable gene clusters corresponding to RGPs.
• Scalability: panRGP analyzes thousands of genomes simultaneously, enabling large-scale comparative genomic analyses.
• Precision and Reliability: When benchmarked against other GI detection tools using a reference dataset, panRGP demonstrated superior accuracy in identifying RGPs and predicting insertion spots.
• Application on Metagenome Assembled Genomes (MAGs): panRGP has been applied to MAGs to redefine borders of known genomic hotspots such as the leuXtRNA hotspot in Escherichia coli.

Scientific Applications:

• Exploration of Genomic Diversity: panRGP enables characterization of RGP diversity within and across species by leveraging pangenome graphs.
• Identification of Horizontal Gene Transfer Events: panRGP aids in pinpointing regions affected by horizontal gene transfer (HGT), informing studies of evolutionary dynamics.
• Comparative Genomics Studies: panRGP supports large-scale comparative analyses to investigate genomic evolution and adaptation mechanisms.

Methodology:

panRGP constructs pangenome graphs from available genomes of a species and uses these graphs to identify RGPs and predict insertion spots, supporting analysis of thousands of genomes.