Best way to find phage genes in microbiome?

Question

[yax]

I have human gut microbial gene catalogue (Qin et al., 2010), I would like to find phage genes/prophage region genes among. What would be the best practice?

Answer 1

[Siva]

You can search your microbial genes against Phage Orthologous Groups (POGs) maintained at NCBI. You will need the COGnitor program from the COG making software COGsoft to search your bacterial sequences against the POGs.

Relevant publications:

• Orthologous gene clusters and taxon signature genes for viruses of prokaryotes.
• Classification and quantification of bacteriophage taxa in human gut metagenomes.

I believe the second publication has used the same data you are referring to (Qin et al., 2010).