proMGE allows the exploration of >16 million MGEs from >670K complete isolate genomes (from species with at least 2 genomes in the proGenomes3 database) and >180K high-quality MAGs from the SPIRE database. At species level, it is possible to explore different MGE categories, their genomic positions, nesting interactions, antibiotic resistance carrying potential, and the extent of their horizontal transfer across higher taxonomic levels (family and above).

Via the ‘Annotate’ page, proMGE facilitates annotation of MGEs in user provided contigs and genomes using a custom workflow , hosted on https://clowm.bi.denbi.de/. MGEs are annotated based on the method described in Khedkar et al., 2022. First, sequences are annotated using a collection of 68 recombinase subfamily-specific profile Hidden Markov Models (HMM) (Letunic et al., 2020) and then the element boundaries are estimated using a universal pangenome approach. Finally, 6 different MGE categories are assigned based on the association of the identified recombinases to specific MGE types.