Community post

Conventional homology-based comparative genomic analyses can only do so much in extracting information from databases. We used phages to test our comparative genomics tool (CALANGO) that considers annotation terms besides sequence data. By focusing on E. coli genomes and prophages, we found that pathogenic E. coli have more prophages than non-pathogenic ones, and genes of viral origin are associated to prophages. Genes annotated as virulence factors are also associated to prophage density, but several are not coded by the prophages themselves. We also found genes negatively associated to prophage presence.

Read our preprint here and try the CALANGO package on your organisms of choice. We are looking forward for your findings, feedback and criticism! I (@Gabriel_MFA) am only a non-coding contributor, so please look for the masterminds behind the project for more info: @_fcampelo and @chicao_lobo.