interpretation of Virsorter output

[sbeiow]

Hi Simon,

I am new in the field of prediction of viral sequences. I am basically interested in detecting the number of prophages from bacterial genomes (including MAGs) and tested your VirSorter software with one test genome. I am though not fully sure if I understand the main output file (see attachment) in the right way: Is it right to interpret that 2 prophages of category 2 were detected in the test genome, because the output indicates two larger fragments on the input contains that punitively derive from prophages? What about the 1052 (=1182-130) indicated prophage genes on the contig VIRSorter_DNA331_NODE_1_length_1298478_cov_95_496415 that do not make part of the fragment VIRSorter_DNA331_NODE_1_length_1298478_cov_95_496415-gene_730-gene_859? Are they spread incoherently across the contig and could they represent 'leftovers' from ancient page infections?

Regards, Sara

VIRSorter_global-phage-signal.xlsx

[simroux]

Hi Sara, Broadly, in the "VIRSorter_global-phage-signal" file, each line will represent a new prediction / viral region. Here, you are correct, two different prophages have been detected, one on contig VIRSorter_DNA331_NODE_1_length_1298478_cov_95_496415 and one on contig VIRSorter_DNA331_NODE_3_length_715734_cov_92_807896. The first two columns are about the contig, i.e. contig name and total number of gene predicted in the contig (here, 1,182 and 663). The, the other columns are about the prophage, starting with the prophage name (which is contig name + starting-gene_end-gene) and the number of genes in the prophage. So the first prophage was predicted to span 130 genes, while the second was predicted to span 40 genes.

Let me know is this makes more sense !

Best, Simon

[sbeiow]

Hi Simon, thanks for your fast response. Yes, now the results make sense to me. Best, Sara