Prophage regions

[niamhlacy]

Hello,

I was wondering how exactly VirSorter defines a prophage regions and if there is a way to get the coordinates of the prophage regions identified?

Thanks,
Niamh

[simroux]

Hi,

VirSorter is using a sliding window approach to find "viral-like regions" within input contigs. When the "best" viral-like region covers less than 80% of the contig, VirSorter then considers that the contig includes both a viral and a host region (i.e. includes an integrated prophage). You can find more details in the original VirSorter publication: https://peerj.com/articles/985/

Depending your version of VirSorter, you can get the coordinates of the prophage regions identified in the file "_global-phage-signal-.csv", or you can get the gene identifiers corresponding to the boundaries of the prophage from the file "_global-phage-signal.csv" and then identify the corresponding coordinates in the file "_affi-contigs.csv".

Best,
Simon