Question

prophage annotations in RefSeq

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3.1 years ago

wkxz ▴ 20

Do bacterial genomes in RefSeq contain annotations for prophages, and if so, where do I find them?

The rationale is I don't want to have to rerun a virus identification tool, like VirSorter2, if this has already been done.

ncbi annotation • 711 views

ADD COMMENT • link updated 3.1 years ago by hugo.avila ▴ 530 • written 3.1 years ago by wkxz ▴ 20

score 0 · Answer 1 · 2021-11-10

Hi, Refseq does not annotate prophage genomes within bacterial genomes, it just annotates phage proteins like capsid and recombinases. Some Genebank files have custom features like "phage region" but this is not consistent. If you want to know if a particular genome has prophages and where they are located, you will have to use another tool as you said. I recommend the PHASTER tool, it's a very good tool, the downside is that it's web based only. Developers do not provide local installation capability which makes it difficult to analyze large datasets. But the PHASTER API can help you automate an analysis of large datasets, so take a look.