A new functionality to search for potentially horizontally transferred genes (HGT) which are gathered in Region of Genomic Plasticity is available in MicroScope.
The PanRGP tool is based on the PPanGGOLiN method.
PPanGGOLiN (Partitioned PanGenome Graph Of Linked Neighbors) computes pangenomes taking into account both graph topology and occurrence of genes to classify gene families into persistent, shell and cloud genomes.
PanRGP applies a score-based algorithm to predict RGPs that correspond to set of consecutive genes that are members of the shell or cloud genomes.
For more information please see:
- Please see this example on A. baumannii AYE
- The tutorial
Prediction of Plasticity Regions with pangenomes